Using a Windows 11 PC, on a USB drive I opened a Cryptomator vault and wrote folders/files into it until the drive was completely full (0 bytes free).
Then I removed some folders (to get a “clean” structure).
But one folder and it’s sub folders remained and can’t be renoved. All files there are gone, so all sub folders are empty.
Tying to delete the deepest sub folder, no specifc error message appears, it just doesn’t work.
The folder has write protection attribute, that can’t be changed. The user access also can’t be changed, but already has full access.
How can I get rid of that folder?
Welcome to the Cryptomator Community 
If deleting a folder inside the unlocked vault fails, you can always just remove the encrypted folder at the vault storage location.
Use the locate encrypted file feature to get deepest sub folder. Delete it and repeat it with its parent folder (locate from inside vault, delete encrypted folder).
If you just delete the top-most directory, you’ll leave a lot of folders behind causing noise in the log and vault health check, because Cryptomator flattens the directory structure.
“Locate encrypted file” doesn’t accept folders, but creating a dummy file inside helps.
It worked, thank you very much!