You're probably going to have to cut away the glass and fine sand the area (very fine like 200 grit) and glass a patch over it. I would mostly sand it clean and not worry too much about the bare wood. Just pray it will wet out not too noticeably. I know one time it was recommended to put epoxy under the blister and clamp it and you can try that but i can't see it making a good wet out or adhesion. If you can lay the deck on its side so any irregularity from the bare wood will puddle with the epoxy.

All you can do is your best try.

I remember years back someone had an error like that and did the glass job patch and then painted a logo on top of it.