will the empeg do anything different with the potentially-bad drive hooked up vs. one that works but is formatted incorrectly (i.e. the one out of the windows laptop)

Yes. On the serial port, you will see it detect the disk drive and then complain about it not having the right partions on it.

and would trying this hose the data?

Probably not, unless there's something electrically wrong with the player that's frying the IDE electronics on the disk (one of the theories we've been working with above).