You can increase the internal ID of an Apple Remote by holding down 
the Menu and Play buttons for about 6 seconds.

Regarding the logical remotes: you don't need to recreate those. 
Instead, press a button on the Apple Remote after changing the 
internal ID and it'll appear in Remote Buddy's hardware prefs. You can 
then assign any already existing logical remote to that new ID.

I recommend to first test, whether your Harmony can truely emulate 
Apple Remote button presses correctly, so that you don't go through 
the whole process just to find out you're facing the same problem again.

Best regards, 
Felix Schwarz