Since the water to cause the rot had to come down through the chainplates, I'd double check the deck before deciding much else. Even if the deck is not wood cored, water can travel along and between the layers of glass causing interesting problems.
Were this my boat, I'd replace the glassed in debacle with good wooden knees blind-bolted and epoxied to the hull. How exactly you shape this depends on whether the chainplates are oriented fore and aft or athwartships.
If you really want to avoid woodword and a proper job, make quite a few small drill holes pointed slightly down, aim a heat lamp at the thing for a few days, and then inject lots of CPES. Frankly this is more expensive and almost as much work as just making a proper knee, but it will turn the wood mush into a cellulos/epoxy matrix of considerable strength and durability and will feel more comfortable to anti-woodies.
G'luck
Ian
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