Jim, after deleting the database/tags/playlists files off the player, you must re-synch with emplode once to get it to rebuild them properly.

It'll rebuild them on-the-fly each boot, but they won't get written to the hard disk unless you synch with emplode.

If you're having trouble with doing that with emplode 3.0, it is safe to go back to emplode 2.0 and use that.