Tom, you really need to get the rotted wood out of there. I've heard of people cutting the deck laminations carefully and peeling them off so they can reuse them later, others replace the core and add new deck laminations and then refinish the deck. I sounds like the areas where your deck is penetrated are not sealed properly with thickened
epoxy. That probably means removing all deck fixtures and sealing the core and rebedding the deck hardware, after removing all wet and rotted core. A very large job.