I'm a bit confused about which drives went into which players. Which one was the primary, which was the secondary, did both players have two drives, did you take only one of the drives with the swap, which one was it, etc.... I can't really understand where the red ball is in the shell game you described. We'll need a more careful accounting of it, to get to the bottom of the issues here.

But before that, please understand that it's not as simple as just plugging in the drive. You've got to follow the procedure carefully. If you didn't do any of that stuff, "well there's your problem".

In a two-drive empeg player, the first drive holds the player software, the database files, and some of the music/playlists, and the second drive holds the rest of the music/playlists. The music/playlist files and their associated metadata files are all mixed together. And because of the way the files are organized, if you repurpose only one drive of a matched pair without formatting it first, you're not going to magically get a nicely organized set of additional songs, but rather, you'll mangle the database and get a messed up system. (See FIDs for more information.)