I want to confirm if it is safe to delete files using cyberduck inside the cryptomator vault on the cloud. If there are any gotchas I need to be aware of.
Well, I recommend to ask that the guys from cyberduck.
https://cyberduck.io/help/
As far as I can see, if you delete a file from a vault using cyberduck, the encrypted files are deleted. No unencrypted versions in the online recycle bin.