This sounds like a job for a 'Pad stopper'. If you search around the forums, I'm sure you can find a copy to download.
Pad stopper is basically one silent note that plays, and stops.
Basically, the idea is, in Registration 2, you would start both the pad Stopper on Multipad One, and the Multipad you want to play on Multipad 2. Pad stopper would end the Multipad playing from Reg 1 while starting the new one in Reg 2.
Alternately, you could save a new Multipad bank with the 2nd Multipad you want to use placed in the first position, and save that to Registration 2. So the new multipad replaces Reg 1's Multipad when you switch to Reg. 2.
Clear as mud?
Adam