btmon,

Check the manual of your CD changer, I know my Pioneer CD jukebox, when connected to a second unit operates in a master/slave relationship. With the CDs in jukebox 1 being numbered 1-300 and the slave unit CDs automatically get renumbered to 301-600.

I then send a remote code to the master (eg. CD 444) and it automatically passes it to the slave unit (there is a 'control' connection cable between the 2 units).

This way, you just have 1 large media list that is 'loaded' onto the master device in the Harmony configuration.