I sugest the following:

Swap good and bad drives so that empeg boots from the good one (your primary is sick, right?) - this is the main reason for partitioning both drives in the same manner, including installing the OS. Your database will be all wrong now, but don't worry about that. Install development image. Install either 'dumb ftp server', or Debian mini-distribution. Use ftp to copy all /drive[01]/fids/* files. (If you install Debian, it might be easier to use ftp client on empeg.) When the drive is fixed, dump everything back, delete files database, fids and playlists from /empeg/var, reboot (don't forget to run ro first) and let the player rebuild the database.

Besides, if you ship the unit to Cambridge, the guys there might be able to rescue and restore the content of your disk if you ask them nicely and if you are lucky that the drive still sort of functions when it arrives there .

Good luck!