Hmm I couldn’t reproduce it with --dry-run. Unfortunately I’ve already ran prune after adding ulimit -n 10240 to my .zshrc profile. So technically it’s not really the same conditions, even without that command. I have added a large ~400GB snapshot by rcloning it, which introduced 199GB of dupes that --dry-run said it will remove.
Going to try it without --dry-run and see what happens.
to repack: 872718 blobs / 412.713 GiB
this removes 358561 blobs / 198.619 GiB
to delete: 0 blobs / 1.327 GiB
total prune: 358561 blobs / 199.946 GiB
remaining: 8319142 blobs / 3.250 TiB
unused size after prune: 0 B (0.00% of remaining size
