It could be a sync problem. If Cryptomator does not find the folder structure in you vault root folder, it assumes that you have opened a new vault. In this case a „welcome“ file is created in the vault.
You can try this:
Use cyberduck to open your vault directly online and thus check if the vault is ok.
If the online vault is ok, disable your sync client, delete the local vault files of the vault that appears to be empty, delete the vault from your Cryptomator app, manually download the vault files from your online storage into the local directory where the sync client should have downloaded it (means: sync your vault but do it manually to exclude possible issues with the sync client), and add the vault again to Cryptomator.