That's why the FAQ (last I looked) still tells people to use Emplode/Emptool to fix the database:

Um, actually, it's not in the FAQ because I hadn't thought of it. Paul's mention is the first I'd heard of it.

So what would be the correct commands for doing it that way?

Let's see, I was thinking of editing that FAQ entry a bit anyway, so how's this for a proposed rewrite:

You should be at a shell prompt now. Enter:

rwm (There will be a long pause)
rm /drive0/var/database
rm /drive0/var/database3
rm /drive0/var/tags
rm /drive0/var/playlists
rm /drive1/var/database
rm /drive1/var/database3
rm /drive1/var/tags
rm /drive1/var/playlists
(Note that some of those RM commands will not work, that's OK)
/empeg/bin/player
(The player application will run and rebuild the databases)
q
(This should exit the player application back to the shell prompt)
rom
exit

Is that the correct procedure? Should that work?