Hi Tonny
Unfortunatly Yamaha refuses to implement a SYNC STOP MULTIPAD function to be stored in a registration. This has been requested since the Tyros 3, when the SYNC START was implemented for Multi-Pads. Though it is obvious that this would be very useful, Yamaha does not listen (again).
Clearly, switching by hand is not a valid option in your case. There's a little trick to achieve what you after. To stop a Multi-Pad by registration, it must load a new Multi-Pad bank, that contains a one-shot Multi-Pad with a single note having velocity = 0 (not sounding). You may download this StopPad:
https://www.dropbox.com/s/cad2jrnu543vngp/StopPad.zip?dl=0which may be used to stop any of the four Multi-Pads. If you want to stop one and start another, just assemble the Multi-Pads as needed, e.g.
Multi-Pad bank A: Sync Start Multi-Pad 1 (your first loop); this is stored in Reg1
Multi-Pad bank B: Sync Start Multi-Pad 1 (containing a copy of the StopPad) , Sync Start Multipad 2 (your second loop); this is stored in Reg2
Hope you get the idea, just ask, if it is not clear.