The Flapper is part of the air intake system located inside the snorkel at the front of the bike. It is shown as part number 15 in this schematic:
The flapper valve opens and closes depending on engine rpm with the standard tune loaded into the ECM. If you load the TOR tune or the Arrow Tune the flapper stays open at all times.
I believe that this flapper was installed to control intake noise to help the bike pass sound level requirements for government certification.
TripleThreat