- The most tedious part of the job I found was cutting new core to fit the section to be repaired. The rot does not occur with convenient right angles. Balsa core cuts really easy with a nice sharp utility knife. At first I foolishly tried to cut it with a saber saw which did not work at all.
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- If you ever have to install new hardware on your deck be absolutely certain there is no way water can come in contact with your core. Overdrill and fill with epoxy. The PO did not pay attention to this so just drilled holes, did not caulk real well and water got in. He even left some open holes in the deck which let water get in very easily. This is where the worst rot was. While I would do this again it is FAR FAR easier to prevent the core damage than it is to repair it.
Reading these two paragraphs in your posting makes me wonder why you
didn't take the opportunity to replace the wet balsa with foam core -- you would not have to worry about wet core in the repaired areas again.
I just had a professional repair a wet section of my deck and he did exactly that.