You'll need to install a developer image. Then, using a terminal application like Hyperterm, access the player via the serial port. Press `q' and hit return to get to a shell prompt. (You might have to do that a couple of times.) (Also, if you have any problems with those first few steps, you should be able to find further guidance in the FAQ.) Once there, type the following commands:
swapon /swapfile
cd /drive1/fids/
rwm
cp * /drive0/fids/
cd /drive0/var
rm database
rom
swapoff /swapfile
Then reboot the empeg and attach via emplode. Both of those steps will take much longer than normal. Sync and you should be good.
Please wait for someone to confirm these steps before you do them to make sure I've not screwed up somewhere.