Dremmel works but go slow and take breaks.
I cut out the top. I know you want to keep the top layer intact, but working from the bottom you can't fill the voids. I tried to remove the top in 1 section so I could glass it back in, but was unsuccessful.1)Take frequent breaks so you don't overheat the Dremmel and burn out the brushes.2)Cut an area bigger than the problem, then dig out under the edge (about 1/2 inch) so when you fit your new core in you can push the wood slightly under the old glass.3)I used 1/4" x 3" poplar from Home Depot and fitted them as tightly under all edges. Sand down any high spots with a power sander and 40-60 grit. Mark small notches where boards fit together every 4-6 inches. Then remove the boards, cut out the small notches and epoxy all sides/edges/ends twice.4)Fit the boards back into the hole and pour first epoxy mix over boards and work it down through the notches to adhere under the boards (flex them to work it underneath).5)Apply several layers of glass mat/cloth one layer at a time (you DON'T have to let each cure fully before starting the next). Work in the resin to prevent any bubbles or gaps. Mine took about 10 layers to fill up to the old fiberglass level. After about every 3-4 layers, I let it cure hard and sanded down any unsmooth bulges/ripples.6)In the upper layers, I added a white pigment so if it gets scratched, it will still be white underneath (like the gel coat).7)When just below the final height stop adding the glass mat and finish off with just the resin thickened with Cabasil (or other thickening agent) to get a smooth surface. Thicken the resin until it is like syrup before adding the hardner and pour it onto the area. Use a plastic spatula to spread it out. If you mixed it to the right thickness, it will smooth itself out without running off before it hardens (takes some practice). If you mess up, just sand it down and try again. You may want to tape around the area to prevent it running off if it is too thin.8)I am now working on a method to create a new non-skid textured surface for the area. Since my 30 year old deck has been painted at least twice, the old texture is no good (I can't make a mold of the old pattern) and I need to resurface the whole deck to get the appearance I want.Remember that epoxy and polyster resins don't have UV protectant like gel coat, so they need to be painted.Good luck,Jim