C-Dory warranty terms were not written as clearly as they could have been.
Nowhere in the warranty terms listed in the owners manual, does it limit coverage to the original owner, nor exclude coverage to subsequent buyers. However, it does state, that the original buyer must return the boat for repair.
Further adding to the confusion, the most recent brochure from C-Dory, states the hull warranty is transferable.
However, Bob raised a valid point - I've heard nothing regarding the new owner's intentions or obligations in this regard. Were C-Dory simply sold to new owners, one might think warranty coverage would follow. However, my limited understanding is only the assets of C-Dory were purchased - and none of the obligations. The boats will continue to be built, but by a different company.
Now...setting all of the above aside, is the rot the typical minor stuff we've seen reported here? If so, it's probably less hassle to fix it yourself - even if it's covered under warranty, and the new owners offer to repair it. It's a pretty simple job, if the damage is limited to the immediate area around the screw holes.