The one catch here is that for uniquing to work properly, all your tunes need RID's. if you are using 2.x on your Empeg, you probably don't have them, but you can get RioRID from http://rmml.dev.java.net (in the Other Karma Apps section) and it will recompute RID's for all your tunes. This may take a while (it's basically doing the process that occurs on import into jEmplode, but downloading off the player instead of reading from the filesystem).
One problem with using RioRID, that nobody's mentioned AFAICS, is that it adds a RID value to the database for everything on your player -- that's 33 bytes of permanently-resident memory per track. If you've got lots of songs on a Mark 2, that might add up to enough to push you over the limit into an un-loadable or un-rebuildable database, especially if you're using any of the player v3 alphas.
Edit: If you wanted to obviate that, one way would be to keep a map on the PC of (player serialno, FID) -> (ctime, RID) so you knew when your cached RID was valid and when it wasn't.
Peter