So you are telling me that you have all files restored but you do no longer have them in the correct directory structure?
In any case you may try to use the sanitizer to restore your vault. You may loose the names of some of the files unless you restore the correct directory structure.
To restore do the following:
- Create a directory vault anywhere you like
- copy the file masterkey.cryptomator into vault
- Create a directory vault/d/
- Copy all the encrypted files into this directory. There should be no files with equal names.
- Use sanitizer to restore your data. Replace vaultPath by the path to the vault directory and replace targetPath by the path to an empty or non existing directory of your choice.
java -jar sanitizer-0.14.jar decryptVault -vault vaultPath -target targetPath