Hi Rory,
I think Kwackboy was more trying to warn you about other implications that can occur, for example if the system acts like a car, then you could not simply swap ECUs due to things like the immobilizer. I work with prototype vehicles and often we can not just swap ECUs due to information being written to different modules that do cross checks.
I'm not sure how the bike system works, but definitely worth a call to a dealer maybe before shelling out for an ECU.
Cheers
Josh