Oh man, you bait us beyond words. :-)
Yep, you can swap either or both ECU's (the 'regular' ECU and the KiPass ECU) but you have to have the KiPass ECU re-coded to recognize the new ECU (remember, no matter which one you swap the regular ECU is new to the KiPass ECU). Any Kawasaki dealer can do it as long as they have the KDS programming system and it seems that most of them do. Not sure what it would cost but probably the same as coding the ECU to recognize a new fob or new TPS sensor- about 1/2 hour of labor. And of course if the KiPass ECU is swapped you will need at least one fob that originally went with that ECU or it cannot be re-coded at all anyway. So for example if buying a used KiPass ECU you have to get at least one fob the ECU was already programmed to recognize or no one will be able to program it to work with the new bike.
Back to the original question, not sure but I think the answers given are probably right: you can swap any ECU out as long as it stays in the same generation bike. Even if the ECU fits the wrong generation bike there is going to be some part of the wiring and / or programming that just will not get along; an early ECU on a late bike with traction control switching for example. Or a late ECU on a bike without ABS and similar. That said, it is possible that you cannot swap certain ECU's between bikes even of the same generation; an '08 ECU with ABS may be different, or at least programmed differently, than an '08 ECU without ABS. My though would be to assume it would not work if buying a used ECU unless it carries the same part number and is known to be compatible.
Brian
Color me stupid here, back is on fire (changing a water pump on ma F250) and brain is frazzled, but, will KIPASS recognize a new/differant ECU? I'm thinking it will NOT work... I'd contact the fine folks at Guhl for their input. If flashing differant ECUs work I can see used ECUs going quick, get one for pure unadulterated power and one for cruising, and one bone stock for potential warranty work