Here's my experience with rotten plywood in an Offshore 33 cabin top. It all started by following a leak and ended up with me ripping the inner liner off. Numerous test holes found that almost the whole cabin top was wet and most of the wood soft and rotten. During the process I found that previous owners had tried to fix the problem by drilling holes from the top down and filling them with epoxy. The standard thought is that the epoxy will penetrate the plywood and firm it up. Epoxy doesn't get past water, all that happened was that there were many, many little epoxy stalagmites in the cabin top. Useless.
It was winter in New York and I couldn't see myself cutting the whole top of my cabin off, so I decided to work from the inside. To do this required a lot of patience and a set of extra hands. It also meant working against GRAVITY. I replaced the plywood with balsa and then two layers of fiberglass matting. Unless there was something I was missing, I could only put up relatively small pieces (maybe 2' x 2') at a time and then had to hold or brace the piece until the glue started to setup enough to hold it. Putting up the fiberglass mat was even worse. It took many hours, and was probably one of the worst jobs I've attempted.
I'm still finishing out the interior wood work so I can't give you a long term status report but I do feel the cabin is as strong as it ever was. A rotten cabin top core made the boat basically worthless, now I feel its marketable again if I ever decide to sell. I would like to sail it again first