So, I already explained how we installed a new bulkhead. After we finished that project, we re-bedded the chainplates. Chances are that at some point moisture had found its way to the deck of your boat around the chainplates. Its not easy to prevent that. This is a pretty good trick for preventing moisture from finding its way through.
Step 1: After you take the chain plates out feel in the hole and see if you feel moisture/ rot. If there is moisture take a heat gun and (without catching the boat on fire) dry out the rot/moisture.
Step 2: If you have just replaced the bulkhead go ahead and install the chainplates where you want them. This will ensure that they are in the right place for rebedding.
Step 3: Once you have the holes for the chainplates drilled where you want them take them back out and put a thin coat of wax (we used a wax toilet bowl ring) on the part of the chaniplates that will stick through the deck. Go ahead and put them back through the deck.
Step 4: Take some epoxy that has been thickened to a peanut butter consistency and fill the space around the chainplate with it. This will create an exact mold of the chainplate and at the same time help stop any existing rot in the deck.
Step 5: Use a polysulfide based caulk such as Lifecaulk, or 3m 301 to ensure that it is completely sealed between the plates and deck. Having an exact mold of the chainplates will make it much more difficult for water to find its way through.