Repository damaged after accidentally deleting data files

Hi @cdhowie ,
I have just had the chance to update my restic version and for some reason I am still facing difficulty pruning my data.

I have rebuilt the index, applied the forget policy and did a prune but the process throws an error in the end.

I have created another topic on the forget policy behaving differently from what I expected it to be, though I am not sure if it is related to this. That topic is here: Curious case of the Forget policy

Please find the output of my rebuild index and prune jobs below:

Rebuild Index:
PS C:\Users\User> restic -r W:\restic\ rebuild-index
enter password for repository:
repository a6a81653 opened successfully, password is correct
counting files in repo
[40:01] 100.00% 67383 / 67383 packs
finding old index files
saved new indexes as [86c92da0 e3f05f6b 17a41a56 b9902f3f 053d414d 6d70fba5 d000c05d 9123c6e1 7aa3246c cbb56b38 3363c07e df46b774 2872fd68 3a911386 6bec4400 fafebbb6 159f9309 fb39d64b 5527f315 e5065eba 4bfa6943 b7ecb72f 684f5e8d]
remove 89 old index files

Forget and Prune:
PS C:\Users\User> restic -r W:\restic\ forget --keep-within 0y1m --prune
enter password for repository:
repository a6a81653 opened successfully, password is correct
Applying Policy: all snapshots within 1m of the newest
keep 1 snapshots:
ID Time Host Tags Reasons Paths
------------------------------------------------------------------------------------------
7e1f669e 2019-02-26 16:13:36 Toblerone FEB,END within 1m C:\Users\User\Documents
------------------------------------------------------------------------------------------
1 snapshots

keep 22 snapshots:
ID        Time                 Host        Tags        Reasons    Paths
------------------------------------------------------------------------------------------
707e4723  2019-04-23 15:23:51  Toblerone               within 1m  C:\Users\User\Documents
                                                                  C:\Users\User\Downloads
                                                                  C:\Users\User\Pictures
                                                                  D:\

019ef9b0  2019-04-24 10:30:01  Toblerone               within 1m  C:\Users\User\Documents
                                                                  C:\Users\User\Downloads
                                                                  C:\Users\User\Pictures
                                                                  D:\

cdd72eeb  2019-04-25 15:45:54  Toblerone               within 1m  C:\Users\User\Documents
                                                                  C:\Users\User\Downloads
                                                                  C:\Users\User\Pictures
                                                                  D:\

bfb5a87f  2019-04-26 13:24:55  Toblerone               within 1m  C:\Users\User\Documents
                                                                  C:\Users\User\Downloads
                                                                  C:\Users\User\Pictures
                                                                  D:\

351fb28f  2019-04-29 09:55:17  Toblerone               within 1m  C:\Users\User\Documents
                                                                  C:\Users\User\Downloads
                                                                  C:\Users\User\Pictures
                                                                  D:\

e10b2206  2019-04-29 10:30:01  Toblerone               within 1m  C:\Users\User\Documents
                                                                  C:\Users\User\Downloads
                                                                  C:\Users\User\Pictures
                                                                  D:\

d1a5e093  2019-04-30 14:14:54  Toblerone               within 1m  C:\Users\User\Documents
                                                                  C:\Users\User\Downloads
                                                                  C:\Users\User\Pictures
                                                                  D:\

4f30bec7  2019-05-02 09:49:10  Toblerone               within 1m  C:\Users\User\Documents
                                                                  C:\Users\User\Downloads
                                                                  C:\Users\User\Pictures
                                                                  D:\

9198acd2  2019-05-02 10:30:00  Toblerone               within 1m  C:\Users\User\Documents
                                                                  C:\Users\User\Downloads
                                                                  C:\Users\User\Pictures
                                                                  D:\

3e0dd2a2  2019-05-03 17:16:31  Toblerone               within 1m  C:\Users\User\Documents
                                                                  C:\Users\User\Downloads
                                                                  C:\Users\User\Pictures
                                                                  D:\

ec592370  2019-05-06 09:46:45  Toblerone               within 1m  C:\Users\User\Documents
                                                                  C:\Users\User\Downloads
                                                                  C:\Users\User\Pictures
                                                                  D:\

cd019f73  2019-05-06 10:30:01  Toblerone               within 1m  C:\Users\User\Documents
                                                                  C:\Users\User\Downloads
                                                                  C:\Users\User\Pictures
                                                                  D:\

29acc393  2019-05-07 10:30:06  Toblerone               within 1m  C:\Users\User\Documents
                                                                  C:\Users\User\Downloads
                                                                  C:\Users\User\Pictures
                                                                  D:\

8583575b  2019-05-08 10:30:03  Toblerone               within 1m  C:\Users\User\Documents
                                                                  C:\Users\User\Downloads
                                                                  C:\Users\User\Pictures
                                                                  D:\

77e2f4de  2019-05-09 10:30:03  Toblerone               within 1m  C:\Users\User\Documents
                                                                  C:\Users\User\Downloads
                                                                  C:\Users\User\Pictures
                                                                  D:\

79035c32  2019-05-10 10:30:09  Toblerone               within 1m  C:\Users\User\Documents
                                                                  C:\Users\User\Downloads
                                                                  C:\Users\User\Pictures
                                                                  D:\

86783039  2019-05-14 10:30:04  Toblerone               within 1m  C:\Users\User\Documents
                                                                  C:\Users\User\Downloads
                                                                  C:\Users\User\Pictures
                                                                  D:\

9fc58c7c  2019-05-15 10:30:04  Toblerone               within 1m  C:\Users\User\Documents
                                                                  C:\Users\User\Downloads
                                                                  C:\Users\User\Pictures
                                                                  D:\

11fcb6c3  2019-05-17 09:57:15  Toblerone               within 1m  C:\Users\User\Documents
                                                                  C:\Users\User\Downloads
                                                                  C:\Users\User\Pictures
                                                                  D:\

77845734  2019-05-21 10:30:01  Toblerone               within 1m  C:\Users\User\Documents
                                                                  C:\Users\User\Downloads
                                                                  C:\Users\User\Pictures
                                                                  D:\

65a677a3  2019-05-22 10:30:16  Toblerone               within 1m  C:\Users\User\Documents
                                                                  C:\Users\User\Downloads
                                                                  C:\Users\User\Pictures
                                                                  D:\

f73b541b  2019-05-23 10:30:04  Toblerone               within 1m  C:\Users\User\Documents
                                                                  C:\Users\User\Downloads
                                                                  C:\Users\User\Pictures
                                                                  D:\
------------------------------------------------------------------------------------------
22 snapshots

remove 22 snapshots:
ID        Time                 Host        Tags        Paths
-------------------------------------------------------------------------------
c9faa05c  2019-02-28 12:23:31  Toblerone   FEB,END     C:\Users\User\Documents
                                                       C:\Users\User\Downloads
                                                       C:\Users\User\Pictures
                                                       D:\

e3ffd381  2019-03-01 15:10:57  Toblerone   MAR,START   C:\Users\User\Documents
                                                       C:\Users\User\Downloads
                                                       C:\Users\User\Pictures
                                                       D:\

afb1c018  2019-03-11 10:34:53  Toblerone   MAR,MID     C:\Users\User\Documents
                                                       C:\Users\User\Downloads
                                                       C:\Users\User\Pictures
                                                       D:\

26898663  2019-03-12 14:47:05  Toblerone   MAR,MID     C:\Users\User\Documents
                                                       C:\Users\User\Downloads
                                                       C:\Users\User\Pictures
                                                       D:\

90400685  2019-03-13 16:53:41  Toblerone   MAR,MID     C:\Users\User\Documents
                                                       C:\Users\User\Downloads
                                                       C:\Users\User\Pictures
                                                       D:\

fa2f2685  2019-03-19 16:30:26  Toblerone   MAR,MID     C:\Users\User\Documents
                                                       C:\Users\User\Downloads
                                                       C:\Users\User\Pictures
                                                       D:\

e4a084b3  2019-03-28 12:11:38  Toblerone               C:\Users\User\Documents
                                                       C:\Users\User\Downloads
                                                       C:\Users\User\Pictures
                                                       D:\

ea18e631  2019-04-02 10:30:01  Toblerone               C:\Users\User\Documents
                                                       C:\Users\User\Downloads
                                                       C:\Users\User\Pictures
                                                       D:\

4d978c64  2019-04-03 10:30:02  Toblerone               C:\Users\User\Documents
                                                       C:\Users\User\Downloads
                                                       C:\Users\User\Pictures
                                                       D:\

8f669003  2019-04-04 10:30:02  Toblerone               C:\Users\User\Documents
                                                       C:\Users\User\Downloads
                                                       C:\Users\User\Pictures
                                                       D:\

e14acf8d  2019-04-05 14:07:42  Toblerone               C:\Users\User\Documents
                                                       C:\Users\User\Downloads
                                                       C:\Users\User\Pictures
                                                       D:\

e49a19ec  2019-04-08 10:30:00  Toblerone               C:\Users\User\Documents
                                                       C:\Users\User\Downloads
                                                       C:\Users\User\Pictures
                                                       D:\

c948dcfa  2019-04-09 12:43:09  Toblerone               C:\Users\User\Documents
                                                       C:\Users\User\Downloads
                                                       C:\Users\User\Pictures
                                                       D:\

d9d344df  2019-04-10 10:30:03  Toblerone               C:\Users\User\Documents
                                                       C:\Users\User\Downloads
                                                       C:\Users\User\Pictures
                                                       D:\

6911cf59  2019-04-11 10:30:04  Toblerone               C:\Users\User\Documents
                                                       C:\Users\User\Downloads
                                                       C:\Users\User\Pictures
                                                       D:\

ffd1ab70  2019-04-12 10:30:04  Toblerone               C:\Users\User\Documents
                                                       C:\Users\User\Downloads
                                                       C:\Users\User\Pictures
                                                       D:\

15a63807  2019-04-15 09:41:51  Toblerone               C:\Users\User\Documents
                                                       C:\Users\User\Downloads
                                                       C:\Users\User\Pictures
                                                       D:\

6fba037c  2019-04-15 10:30:01  Toblerone               C:\Users\User\Documents
                                                       C:\Users\User\Downloads
                                                       C:\Users\User\Pictures
                                                       D:\

b1782998  2019-04-16 12:40:12  Toblerone               C:\Users\User\Documents
                                                       C:\Users\User\Downloads
                                                       C:\Users\User\Pictures
                                                       D:\

db51cd43  2019-04-17 10:30:04  Toblerone               C:\Users\User\Documents
                                                       C:\Users\User\Downloads
                                                       C:\Users\User\Pictures
                                                       D:\

29cfa4b8  2019-04-18 10:30:03  Toblerone               C:\Users\User\Documents
                                                       C:\Users\User\Downloads
                                                       C:\Users\User\Pictures
                                                       D:\

cf5a4fc7  2019-04-22 09:52:12  Toblerone               C:\Users\User\Documents
                                                       C:\Users\User\Downloads
                                                       C:\Users\User\Pictures
                                                       D:\
-------------------------------------------------------------------------------
22 snapshots

keep 1 snapshots:
ID        Time                 Host        Tags        Reasons    Paths
-----------------------------------------------------------------------
464d7afb  2019-02-22 10:05:07  Toblerone   FEB,END     within 1m  d:\
-----------------------------------------------------------------------
1 snapshots

22 snapshots have been removed, running prune
counting files in repo
building new index for repo
[37:56] 100.00%  67383 / 67383 packs
incomplete pack file (will be removed): 00b95d3dbe2837cea815ea7a581b67076beffaaa38086a61242080aed2ed98c9
incomplete pack file (will be removed): 01adbbb734c69f44edc28a6eb9ae32af12066c88a051c0d1373fb0b6e31394b5
incomplete pack file (will be removed): 05f8b33c3cf34b810674ef1ba74aed7b1a8bac124b7ac66c68acb317668698ae
incomplete pack file (will be removed): 08471b76322a1eec5ac4a449b2a85268acf0ad9fa87710ce513b2273d67a6a77
incomplete pack file (will be removed): 091334c8820e89a95b842cb79c56c1b1ef412e010e982c658ed3da626e57fa42
incomplete pack file (will be removed): 0d8532d83351f32da5148fb4c4f29f6b2c3ab89eea8f45ab402f39a49dacff43
incomplete pack file (will be removed): 103bf3d9f8bcc693cfac4594321986025022457bd99be0ca29c510fe291f784a
incomplete pack file (will be removed): 122680b08d3ead87b0cbf7b8eba6578d3d41862f409941715177a1ab697dcc30
incomplete pack file (will be removed): 149dc4a7cb1e16eda5c6ef85d9a76603b49212341f724966587eb5547a92772a
incomplete pack file (will be removed): 16a6efecf06212578d93da2eff64beccda74689419502653669e1b8aa71ba198
incomplete pack file (will be removed): 1702154a54cea939550c9c17fa207bbdda2c87e1cc7e4a130edf94ccd87ecb15
incomplete pack file (will be removed): 1c361b7eee246326fa056a15a2f68b3e44cecdcee5db5dd76add962e991e5217
incomplete pack file (will be removed): 1cfb083bdeeacc4f965c9b2f13ed2a52bb734f14130f3cc2b4a8ac96069ea676
incomplete pack file (will be removed): 1d3e916030782a9d0f436dc427e452686445d5d4ddb8f0e23f7cdbcea367e501
incomplete pack file (will be removed): 1f2ed678442e84d9e3b6753b5b0d3d7fdb84881938ce66aa30c4644c1f11fdd1
incomplete pack file (will be removed): 23ae6618800394d18cf2eafecc6e71d0593123969c29efd0f326a9248df9972e
incomplete pack file (will be removed): 2540d81237718850dcfdbfdef81db763a1da29549352635807a163bbc33297ba
incomplete pack file (will be removed): 27ff0640ea75473b585afdc75375d7230b0d2218cced41b40adc325207e02c0b
incomplete pack file (will be removed): 2d35df290b871691a4cfe1b2af19c3550e01a61143d2a47af451c1444f028222
incomplete pack file (will be removed): 31c1d8ef61bef45f25f99b613c911bcc0fd143e94ea6a140c299b98e2da3c93a
incomplete pack file (will be removed): 31feca6b44962504cc79875f1c9156f1a6e19bdb7db358e1a84c15be8069a514
incomplete pack file (will be removed): 331f37c65819e6de9eb338ae06dbffb0553721f8d148cb65893f861ef6cfa374
incomplete pack file (will be removed): 3ac7a7ec55cf416b9b6278858dea32e849576820d126b4228cad6d7079e4463b
incomplete pack file (will be removed): 41fda4863e93a36b4dc7ab8e4937d67ac68b192c361845b6d630a8496beb3626
incomplete pack file (will be removed): 4554c51ef9ea179ce950161e4d8b8e8f4c134992a23cc87fe3d6ea9b282d03ca
incomplete pack file (will be removed): 48ea114a1c24c6878fbc1dec4e5fa2cbc69cab9058240ad1164d13fa72daf1ec
incomplete pack file (will be removed): 4b3f7eea4a3bd9eb3a8f9096e5021ae15d9e58749f69ff0db92723a32e524649
incomplete pack file (will be removed): 4d80f03c54b26d9c9fa8743d25ea10fdb925d3e83cf790549fe674ef1bb30e82
incomplete pack file (will be removed): 51fa1fd047bcd77c20e47c082043c0fdad5ca9a89a778ec8db73f505d317c552
incomplete pack file (will be removed): 5556bcc838f471a93987253496287387149efa838274cec4e80b669ac35a808e
incomplete pack file (will be removed): 56c046eb5ef2bba09e97fcfdacf93a6e067b4312bcb175143f3173c72056f294
incomplete pack file (will be removed): 5dde82825ef1bec64e0025af8267a88c4cbed71991adf2ddb9314732bf1bcc57
incomplete pack file (will be removed): 5e5ea8738178f87eaf2c8ffbae98be76813c4fab01e2d449b448fabd8f25a328
incomplete pack file (will be removed): 67a05027f14cffe1d7c4c3443aa2a24b06ba2b1795119a6140ad711a46d2b611
incomplete pack file (will be removed): 69d9348fbec7d9ec6b379cfa68f9454cf6d5a6e883fb4d803a089c6cf8dc8511
incomplete pack file (will be removed): 6e0c006c6a110f2552091488338510ba4dd775cdf6b6c286f798f0c1cd5f7641
incomplete pack file (will be removed): 6fe06bb089f13b35228b9c4d4f7ef81b56eb23a2e4cf3324e7c75e2cfe6fbd99
incomplete pack file (will be removed): 78bb3b5675accd8d9580330ac335201c11b1a7c37e9f9570a0e697a2b6db16a0
incomplete pack file (will be removed): 7a9b3f06db315b20544118d62f6ba23b2c7d2853d416399c6dcc695b99f494bf
incomplete pack file (will be removed): 7b60c70cf6fbcd50f3e8341d06b9febf63e7930c5c03b0a67863f54b246bdf0f
incomplete pack file (will be removed): 7c21d7e4fddb9796825b702d3ecfb175cd093537e3c144853f688b13f896c303
incomplete pack file (will be removed): 7cd8f4fff312b94f25770213c1d200acc85fc429daba4e23559a73c382d4f9e9
incomplete pack file (will be removed): 8120af861f6ad0b61a65c10708611b2fc7c75f46d2c3e817ca165c174a6da23a
incomplete pack file (will be removed): 825576997d32a386a8119e70d593cddfa635589663c0a5dcd1a89e406181bef9
incomplete pack file (will be removed): 835de546094f9a107130f6fc1598c528d934d559047fc91a83c0a0bb5699fce1
incomplete pack file (will be removed): 85969c439487d0e9cb44708a0e451efe2cf790e0592d8748d08e53fe2d226c54
incomplete pack file (will be removed): 8685761e6fcd64e864ed57d303a0b7985684a9c94e1cfe580dc144b700baaffe
incomplete pack file (will be removed): 86b9090107be47b6521facebcb0024494113f4fd0355723f87165013168f5879
incomplete pack file (will be removed): 93b600d37de0a53206a77ac5899050ffeb967f3332271d70f82f72b63e59b9a1
incomplete pack file (will be removed): 9511f6f2f05cb3b7b20f08ca7695e771ad90e44d2515454f47c7b13fbce643fe
incomplete pack file (will be removed): 965bc56924f4e565d4c8a73ae3a5021c0b01f8c77dc0fb3d620651e198d89a8b
incomplete pack file (will be removed): 97ef14e114bcb55e9a7e6adddc7a36de63fa49b130498d52fd9602dd5a370a92
incomplete pack file (will be removed): 995885fea4bb26ab2a35a91c4f42971b72f56cf5a5973a40505efd08e529f5e5
incomplete pack file (will be removed): 99fe6b74cd2f049a4716a11a98019435559fe5458cf4b3ce931a819df38f629e
incomplete pack file (will be removed): 9a9bd04992db9abc35af55271bdc462569085bc5f557e98607218d55f940f9f2
incomplete pack file (will be removed): a5e3e96591d5b8f1ff664fcb9f392d6a8d3f2a68817807b449b6b2d5cd44807e
incomplete pack file (will be removed): a9b83d2a53b85971fce6b932cb12fe138d8c678c61aa744e3ccf1776f2da5582
incomplete pack file (will be removed): ad2ed096fb20b70c5b6c812bb015527792e3fd1c68813fa1d1b11b28c9330f40
incomplete pack file (will be removed): ad52757676f09b5f2732781842b41662f3a01f530e4df50596e7b424f9598036
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incomplete pack file (will be removed): c83d92fd41b97d912dba4e90ff51d0e95d70e8ca71c14bf7e9ebd4741de11d87
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incomplete pack file (will be removed): e0b47850d43116edaeca994fb443ec160d53477ef5bdd6b156364b17829333e8
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incomplete pack file (will be removed): e557ec3e88ab92c58e28d8a478a77d2efdcb2b4d5034a8d9ed64d362598d47e8
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incomplete pack file (will be removed): effefee986681b22caedeb9d4d58b4445bd3bdaec85fe4dc7b6080bbcab0567f
incomplete pack file (will be removed): f0df0919bb95f3f7724bd0f72639bf2ff11d814c079e5830c39a21dbcbba72f4
incomplete pack file (will be removed): f46c080b08a4f0a028b121f1daa374f2b4f31ea81daeece259cc9efac61a3264
incomplete pack file (will be removed): f5f8e9a53ced05ed7e3ee5368fdfed10b3db232b5e35219d2002d8ae5480629e
incomplete pack file (will be removed): fb3efd073b85c21717461aa626135e47e1c005f4fbc441d462bd427749670a1c
incomplete pack file (will be removed): fe74838f41ec8aed7777b95a4f043218a22fed6098be633797482128f4d8c21f
repository contains 67287 packs (509507 blobs) with 316.854 GiB
processed 509507 blobs: 4171 duplicate blobs, 4.262 GiB duplicate
load all snapshots
find data that is still in use for 24 snapshots
tree cee759a90802904dcdbe733403dd452f8d709dc637d8fc97b966fc7c07838476 not found in repository
github.com/restic/restic/internal/repository.(*Repository).LoadTree
        /restic/internal/repository/repository.go:709
github.com/restic/restic/internal/restic.FindUsedBlobs
        /restic/internal/restic/find.go:11
github.com/restic/restic/internal/restic.FindUsedBlobs
        /restic/internal/restic/find.go:31
github.com/restic/restic/internal/restic.FindUsedBlobs
        /restic/internal/restic/find.go:31
github.com/restic/restic/internal/restic.FindUsedBlobs
        /restic/internal/restic/find.go:31
github.com/restic/restic/internal/restic.FindUsedBlobs
        /restic/internal/restic/find.go:31
github.com/restic/restic/internal/restic.FindUsedBlobs
        /restic/internal/restic/find.go:31
main.pruneRepository
        /restic/cmd/restic/cmd_prune.go:191
main.runForget
        /restic/cmd/restic/cmd_forget.go:215
main.glob..func10
        /restic/cmd/restic/cmd_forget.go:22
github.com/spf13/cobra.(*Command).execute
        /restic/vendor/github.com/spf13/cobra/command.go:762
github.com/spf13/cobra.(*Command).ExecuteC
        /restic/vendor/github.com/spf13/cobra/command.go:852
github.com/spf13/cobra.(*Command).Execute
        /restic/vendor/github.com/spf13/cobra/command.go:800
main.main
        /restic/cmd/restic/main.go:86
runtime.main
        /usr/local/go/src/runtime/proc.go:200
runtime.goexit
        /usr/local/go/src/runtime/asm_amd64.s:1337

Thank you.