Not really the vault file but in general it can happen, as we encrypt/obfuscate the directory hierarchies, it is possible that a vault folder shows empty if the root folder isn’t synced correctly from the cloud (empty folder) which then appears for Cryptomator to be an empty vault. If the vault file doesn’t match the Masterkey file an error would be shown. So I highly assume as @Michael already mentioned, that something isn’t correctly synced.
You could also have a look into the log file if you see there something suspicious: