I relocated the flap brace to the right spot and re-drilled the flap hinge holes. I then installed some fresh double countersunk NAS rivets at 1/2" spacing to pin the brace to the lower skin per the plans. The brace is sandwiched between the flap hinge and the lower skin, so I filled in the old 3/32" holes with JB-Weld and riveted everything back together. The entire structure is fairly lightweight, so the hidden epoxy-filled holes won't present any issues. Now the flap fits perfectly.