If you just take off the cables and leave the servo connected to do it's thing ,it will be fine,no codes.But you may find you cannot remove the flap with out surgery,in which case you need to wire it in the open position.
The exhaust flap at the silencer ,unlike the gen 1 fazers at the header, are more to do with passing emmisions than horsepower delivery.
On some bikes with it removed and an open can it can cause popping on the overrun.
Most bikes have some form of air injection to burn off unused fuel on the overrun.Part of the flaps duty is to close on the overrun to muffle the pops as the fuel is burnt.
As long as you have the std can with it's many chambers rather than a straight through after market it should be fine.