What am I missing?

It's not a case of what you're missing, but a case of what you've got two of. You'll have a fid 100 on each drive, a fid 110 on each drive, and so on. The only things you'll see from the second drive, are fids which don't exist on the first drive (those will be the unreferenced tracks).

No wonder the database is confused. It won't be sensible again until you've wiped one of the drives.

Peter