Under "normal" riding conditions the ECM will continually update the AFV (add or remove fuel).
I think what burnteyes is suggesting is to re-map the fuel curve to account for the higher exhaust flow.
You should have no trouble finding information on that.
In my opinion, I would start looking for an aftermarket exhaust for the bike. Who knows what kind of hack-job they did on the stock one. Buy an exhaust AND have the ecm remapped. (just my 2c tho)