Replacing balsa core and rebedding hardware
Rebedding: Suggest that you remove the suspect piece of hardware. Take a piece of coat hanger a few inches long, bend an L in the end of it with the leg of the L about 1/2 inch long. Then put that in your drill chuck and stick it in the bolt hole and turn on the drill. The object is to use the leg of the L to remove core material from the deck surrounding the bolt hole. Once the core material is removed and the material surrounding it is dry, put some waxed paper and tape it in place on the inside of the deck. Mix some epoxy and fill the bolt hole and cored out area with epoxy from the top. Once that is cured, redrill the correct bolt hole. You will then be drilling through pure epoxy that is impregnable to water in the future so if the bedding material fails, the seepage won't spread again to the deck's core.
Fixing the bad core: My glass guy does this: From the inside of the boat, he will start drilling a series of small holes in lines in all four directions outward from the "center" of the suspected wet area. Do this until your test hole hits dry core material (in this case balsa core). That will define the size of the area that is a problem. Unless it is very small and can be dealt with as described above, the solution has been to cut out the inner "deck" in a single piece (so when finished it can be replaced). The bad (wet) balsa is removed and fans put on the area until it is thoroughly dry. Then a piece of replacement balsa core is cut to the shape and size needed and epoxied into the void. Once that is complete, the piece of inner "deck" glass material that was cut out can be epoxied back in place and the gaps where it was cut out can be patched (filled) with glass and painted accordingly. Balsa core of the appropriate thicknesses can be found by doing a google search. Then if a piece of hardware needs to be put on the deck, the procedure outlined above is followed so that the bolt hole is isolated from the core material.