I use FreeFileSync as a tool to synch my primary vault with my backup vault. I have always unencrypted the vaults to perform the scan and synch. However, I decided to scan the encrypted vault and compare it to the unencrypted vault. The scan shows 1305 differences and from the best I can tell it appears to be wanting to delete and add files. Unfortunately, with the file names encrypted I cannot make sense of the differences and it appears the file names are different. Yet, when you unencrypt all is good and there are no differences.
Obviously, I will continue to unencrypt and scan and sync. Did the file names change in the unencrypt state at some point that might cause the scan to detect differences while the file content is the same? I believe I recall when there was a recent upgrade of the vault there was a conversion. However, I had to convert both the primary and the backup so I would have thought the algorithm would have resulted in the same file name with date and time?