If you didn't try to add or remove any songs from either player during the "troubled times", it's possible that all the song files are more or less intact. The database might need to be rebuilt by hand, but remember, if you put any songs onto a pair of drives, those songs need to stay in that matched set of drives; that drive pair has gotta stay together as a pair if you want to preserve the songs and be able to re-download them later. As soon as you move a single unmatched one of those drives over to a different player, you've gotta format it if you want it to work.

If you tried to add songs to the player after moving only half the drives around, then you may have toasted some of the songs on BOTH drives. The worst situation would be that now you've got metadata and actual songfile mismatched. For instance, one drive might have FID BF91 which is the metadata for "Rush: Tom Sawyer" and shows that way in Emplode, whereas the other drive might have corresponding FID BF90 which is actual songfile for "Terry Jacks: Seasons in the Sun". So now you try to go re-download that file and actually get the wrong song.

Of course all of the above assumes you can solve any problems with the actual drives or IDE connections themselves, which it sounds like you're still having troubles there.