Hi. As this folder doublets are in the vault, I first think of a process (sync/backup etc) that is misconfigured and is adding these folders into the vault.
It seems unlikely to me that vault files itself are manipulated or the vault is faulty.
If I would find such folders in any of my vaults (and I haven’t in the last years), I would just delete them and check all processes that are adding files/folders into the vault.
To your question:
Actually there’s no sanitizer available for the latest vault format.
Deleting any of these folders will delete the original.
This is something that can be solved with some sanitizer script, but I don’t think it is implemented yet. We’re planning to add some vault sanity checks to the main application in Cryptomator 1.6.0 and this can be added as well.
Basically this is caused by two differend dir.c9r files having the same file content.