The directory structure is obfuscated with cryptomator. I meant one of the level 3 dirs, e.g. d/xx/yyyyyyyyy... . One of these folders is the root directory. The folders in it have this root directory as parent node. If the root directory doesn’t exists anymore, the vault appears empty although there are many files and folders in it but these can no longer be found .
What could help is the log file. Can you take a look if there is anything with error / warning while or after unlocking the vault?