First off, welcome to that club.
I finally got my membership on a fuselage skin. Fortunately for me it will be tucked under another skin where it will never be seen.
I would take some clear packing tape. Put a small piece on another larger piece of packing tape to make a a little sandwich with a spot of no-stick surface on the sticky side of the tape, place it over the unwanted hole, then fill with a dab of JB weld. I did this for all of the tooling holes on the tip-up frame. A little sanding to flush on the outside and you will never see it again.
Here is a picture:
I think that drilling out the misdimple is good and that shouldn't affect the strength of the part (edge distance seems good). Call Van's for any questions about the integrity of the part, but my guess is build on...