I've considered this, but have not tried it:
Sand the one edge of the flap using 1/4" and 3/16" wires. Then shim the trailing edge of the flap up 1/16" (How? I dunno -- I think I'd try a strip of 1/16" balsa, probably 1/8" wide first) and sand using the 1/4" and 3/16" wires again.
Alternately, make sure to do the top parts of both flaps with the first set of wires, and the bottom parts of both flaps with the 1/4" and 1/8" wires. Then think up some jive about why the slight twist in the flap is actually beneficial to the flying qualities of the plane -- I think I'd concentrate on the fact that you're effectively building in a bit of washout into the wing, reducing the induced drag on the inside corners. Since there are more inside corners than outside ones, and since all the 120 degree corners are inside, of course that slight twist is intentional, beneficial, and (by deduction) you are a genius.
Actually, I think that if you get the top surface right and truly get the bottom surface such that the trailing edge is consistently 1/8" thick, then your flap will automatically be right. This will (maybe) happen because you're actually twisting the flap a bit as you sand, correcting any unfortunate tendencies.