Nothing suspicious in the upgrade log. However, we had an incidence with iCloud Drive and Windows the other day and I’d like to verify if that’s the same in your case.
Please open cmd and run these commands.
cd "C:\Users\*REDACTED*~setolabs~Cryptomator\Vault - Documents"
powershell -command "iex \"tree /f\" > \"tree.txt\""
After that, there will be a tree.txt inside your vault. Could you please upload it again? Since all filenames are encrypted, these are not sensitive data. But with that information, I can analyze the vault structure, verify my suspicion, and hopefully come up with a solution.