So, restoring files is a bit difficult. Sorry that this isn’t more polished yet.
Assuming you haven’t changed the backup settings in the control panel, this very long line will help you:
PASSPHRASE=$(cat /home/user-data/backup/secret_key.txt) duplicity restore --time 3D --file-to-restore mail/mailboxes/domain/user file:///home/user-data/backup/encrypted/ /tmp/restored-files
--time 3D says how long ago to restore from.
3D means three days ago. You may have to change that part. This should be just before when you deleted the files. A backup is made each night — hopefully the backup from a few days ago is still there. (It should be. Backups are held for a minimum of three days.)
--file-to-restore mail/mailboxes/domain/user says what files to restore. You should change
user to match the directory path that you deleted.
The restored files will be placed in
/tmp/restored-files. You can then move that whole directory into the right place, like:
mv /tmp/restored-files /home/user-data/mail/mailboxes/domain/user
Let me know how it goes.