Copying the FIDS from two disks onto one disk should not mess up the playlists, provided that:

The two source disks were from the same player.
The two source disks were not messed up to begin with.
The steps in the drive upgrade guide were followed.
The single destination drive was truly blank and properly prepped.
The old source disks were left out of the player when the copying is done.

You wouldn't happen to be running v3 alpha would you? "playlists all messed up" is a phrase I usually associate with V3 alpha.