As I have been working on the refurb of my boat, one of the discovered issues was a series of damaged portions along the deck seam under the rubrail. Nothing too noticeable with everything all buttoned up, but there were a series of previous repairs and some pretty bad areas. Small ones like a pulled out rivet, to a medium impact point, to a very large portion held together with silicone sealer from underneath. Removing the sealant left me with a foot long space.
I experimented with a few methods, but found this to work pretty well. For the small spaces (eventually to re-drill once the top is put back on, just use masking tape along the bottom and edge to hold thickened epoxy that just fills in the space. For the large sections, reinforcement is probably necessary. Masking tape is strong enough to cover the gap and hold quite a bit of resin, and makes a nice smooth underside. So, I lined the bottom with tape and measured out fiberglass tape to both just fit in the gap (two layers) and two layers to cover the opening and into the boat for reinforcement.
I filled the space with a layer of thickened resin (wood flour used), laid in a strip of fiberglass, more resin, the second strip that fit, then a larger piece that covered the whole repair "glued" down with regular resin, followed by an even larger piece to overlap all areas and have good grip on the inside of the hull. Because this space was so long, the weight of the repair was beginning to sag, so I clamped a few this pieces of wood underneath the repair to hold it up in line with the rest of the seam. I wish I had a few more photos of the process, but I was racing the resin cooking off...
Once set, the nice part of using the masking tape is the resin doesn't stick.
Use your sanding device of choice, and pare it down to fit the profile.
In comparison to the rest of the seam, this repair seems just as flexible as the areas nearby, is quite strong, and provides a nice flat surface for gluing the top deck back on. I have a few more pictures of some of the other repairs, tried a few different methods, but this masking tape method seems simplest and was not too hard to do.