Is there anyway I could dump the mp3s to the PC in such a way that I could restore a player with playlists preserved?

Yes, as Mike said, you could use riorid.jar and riobackup.jar to calculate RIDs and backup/restore the playlists separately from the tunes. Thanks to Mike, this has the advantage of working cross-platform, meaning you can back up the playlists from the empeg and restore them to the Karma or the Central. I've done both, and it works.

But if a simple file-by-file preservation of the empeg's contents is what you're looking for, then simply FTP'ing the entire contents of the FIDs folders on both drives is all you really need to do. (Remember, playlists are FIDs too). This is even outlined in the FAQ here.