I had a similar problem with a boat a few years ago. Just a rub or thinning of the gel coat is not a problem that will necessarily cause a leak (maybe water bubbled fiberglass years down the road), but if the fiberglass under the gel coat is cracked, even ever so slightly, it will. Even the smallest of cracks will cause the boat to take on water. The only way to fix it is to grind and sand it all the way through and back in a bevelled fashion (to integrate it to the existing) to solid, undamaged fiberglass and then layer after layer of patch to fill and build back up what you took out. Let dry, sand smooth and paint. There are no shortcuts. I finally learned that after doing the same repair three times.