First of all, understand that temps as low as 140 degrees Fahrenheit can still be hot enough to permanently damage the epoxy resins used for most wooden boat work. Don't put a heat gun to anything you aren't trying to remove and planning to replace. It is just asking for trouble. If you have to refinish badly messed-up gunwales, it is probably worth taking them off, cleaning them up and then putting them back on.
There is nothing you can put on the bad glass which will make it all go back to clear. The proper fix is to sand the fiberglass off in that spot, feathering out the edges. Then patch the spot with new fiberglass cloth and epoxy, overlapping the feathered edge. Fill the weave with multiple coats of epoxy resin and then sand it smooth, feathering out the edges of the patch where they overlap onto the original fiberglass. Finish with a good UV resistant varnish. Be aware that fiberglass is pretty hard and the wood under it is pretty soft, and that the damage to the glass likely goes all the way through it. The trick is to sand carefully to remove the fiberglass, but not dish the softer wood as you finally sand through the last of the glass layer. Color match may not be perfect as resin, varnish and wood can all darken a bit from the sun over time, compared to fresh fiberglass work.
Plan B would be to hide the spot with some sort of painted graphic, and maybe do another one on the other side to make them look like they're supposed to be there. The damage isn't likely to actually cause serious structural issues or be in a critical area, so it probably isn't going to be much more than ugly. This plan would be a hell of a lot less work than patching, so it's worth pondering the options a bit.
