I created a new vault and synced my files with FreeFileSync into it.
I noticed that it complained that it can’t delete its temporary files.
I opened it in windows explorer and Cyberduck, but I couldn’t delete the files as well.
Cyberduck gave me the name of the actual file in the vault. I checked and its ‘read-only’ attribute was set.
After removing the attribute, I was able to delete the files in windows explorer and Cyberduck.
So, for some reason you can copy files with the ‘read-only’ attribute into the vault, but once in there, it cannot change them anymore.
Starting Cyberduck or Cryptomator as Administrator didn’t help.
Reported and acknowledged here: https://github.com/cryptomator/cryptomator/issues/776
Thanks for the tip to delete the read-only files.
I posted now a Workaround: Windows: How to remove write protection from a file inside a vault