This could have at least to possible reasons:
-
As mentioned in the quoted message
Have you made sure that both vaults have been created with the current cryptomator version or have been opened before using this version? By current version I mean Cryptomator in version 1.5.x
-
You have not only lost the
masterkey.cryptomator
but at least also the root-folder which causes the vault to appear empty. This could be checked with the sanitizer which is still being made fit for the current version.