I believe the planes that sport the new effects system (B-25 comes to mind) will actually leave the flap on the aircraft and make it look ragged. The ones using the old system have an "on or off" system; if a system is functioning, it's intact. If it's become non-functional, it flies off or leaks (fuel, oil, radiator). Flaps in this game can't be destroyed, only disabled. Regardless of what aircraft you're flying and regardless of visual effect, if your damage list shows a flap in red, it's jammed in the position it was in when it became red.