I find its best to lose a flap when they are up. It feels like when u lose a flap in the down position,the result of the damage is not that the flap is gone, its that the ghost flap remains, stuck in the position it was when it was lost. You cant see it, but its there.
Maybe its meant to feel like it the affect of when you lower your good flap, it feels funny with the other one missing, but to me it feels like the flap is still in the position it was when it got blown off. Try it sometime at flaps up, and again at full down when u take damage.
PS Flaps are the first to go on me...ALWAYS. 80% of the time left flap. Which is fine for me, because its still flyable, unlike a 109 whose radiator goes alot.