In the more recent graphical updates when you "lose" a flap or elevator, the remnants (ribs, tattered material) are in fact still there.
It's just that it's going to be a while before every plane is up to this new evolving standard of eye candy.
If you look back in the forums you'll see folks asking (for many a year!) for 2 flap settings, "stuck" and "gone" -- instead of this combination of the 2. I was/am one of them.
Now that we have "surface damage" as well as part damage, has anybody noticed anything new with the flaps? Can they be damaged without jamming? Do they lose lift?