The FAQ says:

Put the player's hard disks back into read-only mode (don't forget this!).

Reboot the player (it will rebuild the database files on its first boot)

You'll then need to connect with Emplode/Emptool/JEmpeg and get it to rebuild the database too. The database gets written to disk when the PC rebuilds it, but not when the player rebuilds it (*). Until you sync using Emplode/whatever, the player will rebuild its database on every startup.

Peter

(*) The player will, in fact, write the database to disk if you start (not reboot) the player with the disks read/write. But you can't easily do that except from the shell, so Tony's instructions are more foolproof.