I am using Cryptomator on my Synology via an SFTP rclone mount. Since I am using a union mount to combine multiple drives into a single visible volume, and applying aggressive filename shortening on the Cryptomator side, I occasionally encounter errors like the following:
20:38:51.002 [Thread-28] WARN o.c.cryptofs.CryptoPathMapper - Did not find valid content inside of /storage/cryptomator/Testownikow/d/A4/CK3UEOXADOKQHBHHUVRBFQYDGTE5VC/4ICbx4aXzprMGaJACMGX9MPrrGiYuQ==.c9r
20:38:51.003 [Thread-17] WARN o.c.cryptofs.CryptoPathMapper - Did not find valid content inside of /storage/cryptomator/Testownikow/d/A4/CK3UEOXADOKQHBHHUVRBFQYDGTE5VC/fcWz1e0EO_G1cz3khTvIFRkoWy4=.c9s
This indicates that there are corrupted files which cannot be removed, renamed, accessed, written to, or read from via the Cryptomator mount. In my experience, this typically happens in one of three cases: either the directory is empty, it contains only a name.c9s file without any actual content or name.c9s or content.c9s files are empty.
To address this, I created a small script to automatically delete such corrupted files: GitHub - nikow/fix_cryptomator_vaults
In my setup, the script runs from crontab. I sincerely hope you never need it - but if you do, this might be the solution to your problem. I made it public because a friend of mine decided to stop using Cryptomator due to similar issues.