So you have 2 ECUs both from a 2006 2.0L SC LSJ engine? I don't see any reason you can't swap them out. I plan on doing this too, one ECU for E85, the other stock one for E10 gasoline.
The first while you put the other ECU on your engine, it will be learning the engine. You might have to do the knock sensor relearn, maybe a crank sensor relearn, it will be modifying the short term and long term fuel trims.