I was about to suggest removing the offending playlist files (for real, from the empeg filesystem), but that would left its parents with a missing child. How about deleting all the playlist content from emplode, syncing, and then repopulating the list from refs=0 search result?

What happens when you delete database, playlists and tags from /empeg/var, mount drives RW, and restart the player by exiting the shell? It should rebuild the database and write it. Subsequent syncs should be OK...