Does the unlocked vault still show data on the linux machine?
Due to an unfinished/incomplete sync it can happen, that Cryptomator creates a new in-vault root, causing that the whole vault will be displayed empty.
To test this, you need to find out which path in the vault storage location contains your vault root. On the computer, where the vault is not broken, unlock the vault and place a file inside it at the top directory. Your cloud provider should notify you that an (encrypted) file is uploaded. Its file path points to the vault root. On your other computer, where the vault is broken, check if this filepath is also present. (inclduing the file!)