Once the flaps were drilled I had two options on how to retain the hinge pin so that it won't come out. I chose version two with a slight variation utilizing a screw, plate nut and pieces of hinge.
3 “eyes” were removed from the center of the hinge and the pin was split at that point. The pin was bent at 90 degrees and then again to match the angle of the flap brace to insert into the pieces of the cut hinge. The whole assembly secured to the flap brace with a #8 nut plate and screw. This worked out fantastically and am happy with the results, although the bends were a tiny bit tricky to get right. This should hold them secure and provide easy removal down the road.
I also had to countersink the flap brace to accent the dimples in the skin and keep the area flat for the hinge. No problem here, drill with hinge in place to keep the countersink bit from chattering.