Should I also synchronize masterkey.cryptomator? I mean would that leak my AES key?
So the Masterkey is encrypted using masterkey.cryptomator using RFC-3394?
masterkey.cryptomator contains the encrypted (or wrapped to be more specific and yes using key wrapping specified in RFC 3394) encryption/MAC masterkeys. More info on how that works here: https://docs.cryptomator.org/en/1.5/security/architecture/#masterkey-derivation