You definitely want to remove as much of the rotten core as possible. While, GitRot is a good product, having a solid thickened epoxy in there instead is probably better for the deck in the long run. You also want to dry out the area as much as possible
I made up a few bits in the machine shop for ripping out the core that look kind of like a T with two sharp chisels on the ends of the crossbar. It seems work better than the makeshift ones, as it is better balanced and easier to control as a result.
Once you've reamed out the rotten core and dried out whatever good core is there... fill the area between the two skins with epoxy thickened with high density filler or collodial silica. Ollie's suggestion to use a syringe is a good one, as you don't want to have any air bubbles or voids. The way I've done it is to drill several small holes at around the edge of the reamed out area and then to inject epoxy into the holes until it comes out on the other sides.. The thickened epoxy serves two purposes: 1) it acts as a solid compression resistant filler for the deck fitting to be tightened down on—which balsa and foam core materials don't do well...they compress; 2) it acts to prevent water leaks around the fitting from migrating into the deck core and causing damage, core rot and delamination.
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You know what the first rule of sailing is? ...Love. You can learn all the math in the 'verse, but you take
a boat to the sea you don't love, she'll shake you off just as sure as the turning of the worlds. Love keeps
her going when she oughta fall down, tells you she's hurting 'fore she keens. Makes her a home.
—Cpt. Mal Reynolds, Serenity (edited)
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