Hey, I’m sorry that you had a problem with restic, we don’t really handle this workflow well. What restic is telling you (during prune and also during check) that snapshots in the repo reference data that just is not there. I may have happened when moving the repo around, or fsck on the disc did not discover a file or so.
It should not be a problem, since the snapshot (which references the data) is created as the very last step. So if you make a copy of a repo while a backup is running and then inspect this repo, the new snapshot won’t be in there, and it’ll just have some data that isn’t referenced anywhere. All snapshots should be complete and consistent.
In order to be able to run prune again, you need to remove the snapshots which reference the missing data. That’s not optimal, but works for now.
The restic check tells you which trees reference the missing data, e.g. c80b0385. You can find out which snapshots reference this tree by running:
$ restic find --tree c80b0385
It will (among others) tell you which snapshot references this tree. You can then use restic forget to remove that snapshot, then run restic check again to check if there are more references for the missing data.