I suspect that the files are still in your .snapshot directory. You can use telnet/ssh and copy the files into the domain directory… And the user that you use to FTP into your domain would have to be set up with shell access. (I can explain in more detail how to do this if you need)
Alternativly you can just get into that .snapshots folder with an FTP program and download everyting, then re-upload into the correct place.
But ya, it’s not going to re-appear on it’s own at this point.