There was a bug in the implementation of the lock-free deduplication algorithm, which failed to include some new snapshots when determining which fossils are still referenced by snapshots to be kept. As a result, some fossils still referenced by these new snapshots will be mistakenly deleted leading to the ‘missing chunks’ problem.
If you’re running prune and backup jobs in parallel, this bug may affect you and you should upgrade to 2.1.1.
Also run a check command on all snapshots and all storages to make sure there aren’t any missing chunks.
duplicacy.exe check -all
This bug is fixed by this commit included in the 2.1.1 release: