Simply copying the files from two drives onto one should have been fine.

Playlists are merely files like music files but are simply a list of more playlists or files rather than MP3/FLAC/OGG data.

The filenames are numbers (called FIDs). They are unique across the two drives so there should be no conflicts. The empeg doesn't even care which drive the files are on. It just looks on both drives when looking.

Define what you mean by "messed up"...

edit: technical info here on FIDs here (and on the link):
http://www.riocar.org/modules.php?op=mod...;faqent=133#133