I spoke to Suzuki Australia who informed me of the following:
1) The key has a magnetic device in it that matches up with the ECU. When a bike is manufactured, the ECU is 'uncharged'. When you insert the key for the first time and turn it, it sets the ECU. After this, the ECU will only work with that key.
2) If the keys are stolen, it is recommended to change the locks anyway. That's a no brainer. However, as the existing ECU is matched to the previous key, the ECU has to be changed as well.
3) If an ECU breaks down, when you install a new 'blank' ECU, using your old keys will set the immobiliser on the new ECU.
In a nutshell, losing both keys, or having them stolen, means replacing the lockset AND the ECU.
This is what i've been told by the experts at Suzuki Australia, who also deal with Suzuki race squad in Australia.
I asked them if the existing ECU can be reflashed, and they said it could probably be done in Japan, however, Japan do not want to have anything to do with reflashing ECU's that have been installed on bikes.
Seems i'm out of options here guys, but I haven't given up yet!!!