I use duplicity to backup things without using the Zentyal web interface to do it.
Typically, if the destination you backup to is the same each time, duplicity will do incremental style backups. In other words, when you try to restore, you can not only restore the latest versions of files, but you can also restore previous versions of files as they were at the time of a previous incremental backup. This means you should be able to restore files that are currently deleted.
However, in the command you are using to restore, you must specify a time in which the file existed. Your command doesn't specify a previous point in time, and since the file was deleted at the time of the last incremental backup, you cannot get the deleted file without specifying a time at which it existed.
I think your command is missing the -t argument. Read about that in the man page for duplicity, or take a look at these examples:
https://help.ubuntu.com/community/DuplicityBackupHowtoFor example, if you know the file existed during a incremental backup that occurred 3 days ago, you might try adding -t3D or -t4D to your command, and see if that will restore the deleted files.
edit: I'm sorry, I do now see that you did indeed specify --time. Perhaps you can try a higher numbers than 3 days and see if that helps.