My hull-deck joint is same as OP's' larger fasterners holding the deck to the hull flange with smaller fasteners holding the toerail through both the deck and hull flange.
My toerail is adequately weathered/worn so as to be minimally serviceable in a couple spots, and I have maybe 6-8 toerail fasteners that leak on a rare occasion. These fasteners are frozen somehow in place where, even if I could easily remove them, the toerail needs to go.
I was going to remove the toerail and glass the joint inside/outside...glassing everything in (i.e. all deck-hull fasteners). With 6-8 layers glass inside and out (a common technique) this does lend structural strength. But I've come up with a different approach that I was to undertake before the Covid stuff came up.
New plan that is easy-ish but not aesthetically acceptable to many perhaps:
-Remove toerail and toerail fasteners.
-Clean-dry holes produced.
-Into holes place flanged FRP bolts
with FRP washer over deck/under hull flange with FRP nut. When placing these fasteners, set with quality flexible epoxy (=no way for water
ingress about these holes in the future).
-After epoxy is set, grind off the head
of the bolt...leaving the flange of the bolt head
to maintain capture on the underlying washer.
-Fair-in the top-side FRP washer/bold-head remnant to suit and/or somewhat hide under a new toe-rail solution.
-While I'm at it I'm going to glass 3 layers of the bottom/inside of the hull-deck joint.
Otherwise, I will do some type of "from the outside" reaming/digging of the joint as described by SVQofP...wherein I'll place some quality flexible epoxy. But no glassing of the outside of the joint (a biggie to me).
Importantly, the edges of my deck are solid fiberglass
such that I'm not concerned about water
ingress from about the hull-deck joint migrating into wood in the deck.
For a future toerail I'm undecided on a few options...but if I go back to having any wood affixed to the deck topside, I'll embed FRP threaded studs into the deck poking up /through whatever wood I use. I really, really don't like metal fasteners around/through this joint (or through the deck in general).