Get a shell either via the serial port, or by installing telnetd (it's possible, by the way, to run the devs script for telnet via hijack from config.ini; just remember ro run "rw" before it, and "ro"after it), and go into /empeg/var and remove the database. Then, hopefully the player rebuilds the database again when it restarts. Then, synchronize again.

If that fails, ftp off a copy of the database and some sucker (perhaps me) can try it on their player and see if it results in horkage.