Finally some progress after holidays, a string of bad weather and a sinking dinghy that needed to be repaired.
I managed to cut out the old ply and bed in a new ply core on a bed of thickened epoxy.
I pre-wet the ply and the old glass with unthickened epoxy, then spread a bead of thickened epoxy then temporarily screwed the ply in place until the glue dries.
The big holes in the ply are where the chainplates will pass through. I'm going to fill the holes with epoxy and then cut the correct through deck holes. This way there will be no ply exposed to any water ingress.