Now that I've got a few extra minutes to reply, I'll clarify in more detail.
The player does not store the files onto its hard disks in a nice, clean, easy-to-interpret manner. It stores them as
FIDs, and each song file, as well as each playlist, gets two FIDs. One is a data header, the other is the actual data.
To further complicate matters, emplode makes no attempt (in a two drive system) to keep a given set of songs and the corresponding playlists that contain those songs, on the same disk drive. In fact, it
drops the songs and playlists onto each of the two drives somewhat randomly.
To even further complicate matters, when emplode is dropping songs and playlists onto the drives, I don't think it even makes an attempt to keep the "0" fid and the "1" fid on the same disk drive. Meaning, that the data header for a file, and its corresponding actual data, might end up on two different drives.
What this means: if you feed the player one-half of an old matched pair of loaded-up drives, you will be getting a shotgun random half of the data that was on the player. Including the very sticky situations of data headers without the corresponding actual data, playlists that point to songs that no longer exist, and songs that existed in playlists that no longer exist.
Finally, if you attempt to pair up an old data-laden drive with a new drive that has at least some data on it (I don't know if your big drive had been fed any songs prior to the old drive being added back in), you will get the extremely sticky situation of more than one file that has the same FID. And there's not even any guarantee that the two files sharing the same FID would even be the same type of file (playlist/song).
So, as you can see, by putting half of a matched-pair back into the player, you've really toasted the database.
If you hadn't tried to synch any new songs into place after having done that, I would say you might be able to get away with just wiping the old drive clean (without erasing the new drive), deleting the database files, and doing another synch. But since you said you tried adding some more songs after you noticed troubles, then all bets are off and I'd say it's time to dust off and nuke the site from orbit. It's the only way to be sure.
There's one final thing that's worrying me, which is: You said you did this upgrade because you started noticing disk troubles with your existing disks. But you didn't say what steps you'd taken to repair those troubles prior to adding in the new disk drive. So I'm worried that we might be dealing with multiple simultaneous problems.