Her transom is the same way, about a 1/3 of the filler broke out with the good wood on the port side, about 3/8 thick, and some was bonded to the wood, and not to the transom at all, and there were also big voids just like you described, and Yes .. a Pain to get flat again. When I get the rest of the wood off, I will mix up a chopped strands and resin filler, use that to get the transom flat again, then I will bond a 3/4 plywood piece about 6 inches wider at the bottom than the top, the next plywood bond will be the one that extends to the sides of the boat, the third bond will be 3/4 ply about the size of the transom box, thats the way I buiilt the transom in my Scimitar. I took a break from the transom today and layed in the first section of floor, injected more foam so it will get it's expanding done, I will lay in another section tomorrow, inject more foam, then go back to the transom.
Here's a few pic's of the transom build in my boat.