This is a pain in the ass! It doesn't seem there is any support for this in iFolder. If you copy a file back to its original location on the iFolder server, the user can not sync it back. I guess this is because all information on what to sync is in the simias database.
However, I found a way to restore single files. But this didn't work if the entire iFolder was deleted.
Send the restored encrypted file to the user. Tell the user to add it in the original folder location and force a sync. This will make the file double encrypted on the iFolder server. After the sync is complete. Tell the user to revert the iFolder to normal folder. Replace the double encrypted file on the iFolder server with the restored encrypted file. Then tell the user to download the folder to a new location. The encrypted file will now be decrypted on the client.
Now the user have to fix up the mess with two different folders with almost the same content.
I hope there will be some kind of fix for this in a future version of iFolder.