Yes, you just copy the fids directory.

If everything is operating normally on the empeg, then the files that exist in the fids directory on both drives should be unique. You should be able to combine the fids folder from disk0 and disk1 together onto a new (larger) single hard disk, and theoretically there should be no conflicts.

There are some pieces of information that you will lose if only the fids folder is copied. The fids folder has only your playlists and songs. Other settings are in other places.

For more information about backing up and restoring the player, and saving those other settings, look here.

Please note that you don't have to back up your files onto an FTP server like that if all you're doing is installing new hard disks. The drive upgrade guide has full instructions on how to do this in situ.