So, for the sake of anyone who might be interested, here is a sketch of the method I am using to repair wet spots in the cabin roof of an O'Day sailboat. Step one, I used a Fein tool to remove the inner shell and then the inner layer of the top proper. the damaged balsa was scraped out, the top layer prepped and coated with a layer of epoxy.

I have explained my method of encapsulating every piece of end grain balsa. This ensures that it can not get wet again.

I back fill the void between the actual top and the inner shell and then grind it back in order to get a good bond.

So I keep showing the bad area by the hatch. I have pretty much finished filling, I used a long board to get it straight and now I am at the fine sanding part of the program.