If the balsa lamination is soggy and rotten I would remove the balsa lamination and replace it with ½ plywood that has been coated with epoxy. You could probably remove the soggy balsa with a electric chain saw and not damage the top or bottom glass to badly. Looking at your new pictures it does not seem like you soaked the new wood with epoxy before you put it into place. How can you prevent that new wood from rotting and soaking in water if you didn’t protect it first???
FellowShip
Just for the Grins