You also need to prune all the contents of /drive0/fids and /drive1/fids. Then do a synch with emplode and it should be OK after that and ready to accept a fresh set of tunes.

Hm.You might also need to do this.

Anyway, the only reason I'm suggesting that is because it's a shortcut past running the builder software, and that's what you asked for. Otherwise just run the builder and install 2.0 fresh.