When you said :
"Cut through the deck, remove the core and I would think it very unlikely the boat would go back together again neatly. I would be very concerned about deformation of that remaining thin skin before the repair can be completed."
I agree with you that if you don't pay attention when you redo the fiberglass work you will end with a deformation. I did the recore by removing the top layer of fiberglass, i (we) just finish to laminate the fiberglass. If someone want to do it(I discourage them, i think the epoxy filling can do the job) the key to succes is to take your time. My sequence was: Remove the top layer, remove the wood, grind the remaining of wood, put at most two layers of mat, wait until it's dry, THEN in my case i put a layer of corecel glue with polyester resin, wait until dry, then 2 layers of mat, 1 layer of roving, 1 layer of mat, 1 layer of mat, 1 layer of roving, 2 layers of mat. All 8 layers was put 1 after 1 after one in the same time, we worked ( me and my helper) fast. We rolled only when all layers was put on the boat. I can confirm that it's a doable job BUT I did it only because i hired a specialist, my helper is a professionnal and i'm the amateur.
Even if you recore the deck with the epoxy way, take your time, don't go too fast because you will for sure deform the liner inside the boat, the skin is so thin, it's unbelievable.
I have a lot of pictures of the work, i will try to take the time to send it on the pictures gallery
So the key to succes is patience, take your time.