There shouldn't be core around the through hull. Our Gulfstar is a cored hull but there is about a 1 foot square area around every through hull that's solid fiberglass. It's easy to see as the hull thins out and has a depression around each through hull.

I would think that you could remove the through hull, cut out the inside fiberglass skin along with the balsa that has deteriorated and build up the fiberglass making it solid around the through hull flaring the new cloth over the adjacent cored hull. It would be an easier fix and would end up being as it should have been when manufactured.

Good call.