Chances are you cant "reflash" your ecu. You will probably need a new chip (or a new ecu with said chip). Injectors work off of pulse width(length of time electricity is applied to the injector to determine how long the injector is open/spraying fuel for) to determine how much fuel gets sprayed in your combustion chamber. So a larger injector, using the same pulse width will inject more fuel. Therefore, it will be out of tune.