I had this (or a similar) problem (where emplode no longer sees anything on the empeg, and the empeg has no visible playlists at all from the front panel).

Removing (I believe, mac can correct me if I'm wrong) the files in /empeg/var/ (the directory which has the "database" file in it, with a few others) and then letting the unit rebuild the databases solved the problem for me.

ObDisclaimer: I don't have a 100% clear recollection of it, I could be wrong, sanity check your work. Don't blame me if your unit fails, I don't work for Empeg and thus am not permitted to have a clue how it works or what will happen if you bone your unit. :)