I said the exact same things you said on an earlier thread about a month.
Stupid question. Have you check out latest JEMPLODE? There is a beta version of a USB interface that seems to work OK for downloading from the EMPEG. (Haven't tried uploading though) and even creates a directory structure like that on your Empeg when it downloads the track.
Only caveat is the case where you have same tracks in different playlists. I think it skips duplicates but I'm not entirely sure. You still won't have a perfect copy of your database.
It should go some of way of accomplishing what you want, though.