I had a similar issue with through deck penetrations for rigging attachments allowing water to get into the ply core, cause rot and delamination of the deck. I ended up cutting out a section of upper side of the deck, digging out the rotten ply, glassing in a new core and laminating a new top section. Then I built new bulkheads and through deck chain plates to strengthen everything. I also made sure that when I did this, I cut the ply back from where the chainplates would pass through and back filled with epoxy. Any water leaking around the chainplates will not be in contact with the ply core.
I have gone down the road of building up a fillet of butyl mastic around the chainplates and that seems to help, but is not 100% effective. The only way to stop the leaks is to put chainplate covers on the deck with sealant underneath. (
www.rigrite.com/Hardware/Chainplates_&_Stemheads/Chainplate_Covers.php)
I have the covers, but haven't installed them yet as it will need me to pull the mast down and disconnect all the rigging.