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.