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You did not mention if you coated the wood dowels with an epoxy or polyester resin which would secure the dowels and seal the repair. Maybe you just missed this step or you forgot to mention it? If water was present I would have used epoxy to seal the dowels/repair. After sealing the repair then you would repair the gelcoat.
Gelcoat does not stick to epoxy very well so you might need to sand/grind down the epoxy so that area is lower than the surrounding area and then apply polyester resin and then your gelcoat. Others might have a better idea but that is how I would repair it.