/empeg/var/ is actually a symbolic link to /drive0/var
so its quite normal that you 'ended up there' even though you went cd /empeg/var

When you mentioned about copying all the files using the LB (Lazy Bastard) method did you rename any of the files in the fids directories on your source empeg?
If so, then the playlists etc wouldn't work anymore as the files in the /driveX/fids are all named in a particular way and the files should not be renamed.

You also must ensure that both the *0 and *1 files are moved together as the *0 file holds the mp3 files (and playlist) (i.e. what you play), but the *1 file holds the tag information which the database rebuilt from.

I assume you have empetied out the /driveX/fids directories on your destination empeg of all files now right?