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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.