Regarding my third question: Cryptomator always creates a backup of the masterkey file after a successful unlock. There were rare cases about “empty” vaults if the masterkey file didn’t match the encrypted vault contents. It happened because somehow the masterkey file was replaced with a different/unrelated one.
That’s why my idea was to check the version number inside of each backup file and if there were multiple ones with version: 7. If that’s the case, you could rename and try the different masterkey file(s). But be aware not to just use one with version: 6 or lower because once you’ve done a vault upgrade, the upgraded vault contents are incompatible with lower versions.
And I assume that you’ve already checked if the size of the vault is somewhat reasonable and there should still be some data?
You could enable debug mode, unlock your vault, and check if there any suspicious messages that might hint at the unexpected behavior.