Ooof… that’s rough. If it were me, I’d just sand and patch the bubbles. I had a few blemishes that I just couldn’t live with. Here is one of those where a thread from a towel I used to wipe it down somehow got caught and I didn’t catch it before putting the glass on. When everything cured it had created a bubble and to me was just an eye sore (I mean who wants to see such a thing in their finish, right?). I sanded it down and far enough out to make a good transition, then I laid two layers of a patch at the same time (since it was on the top). The effort was minimal at best and the end result is that you would never know tell it was there.
If you DO decide to remove the glass entirely from that side, I’d recommend a heat gun and a scraper/putty knife. It makes quick and easy work of removing epoxy/fiberglass (there might be a video or two out there on it). It will just peel right off. Just go slow and be careful not to damage the wood and of course sand/feather out the edges so that it blends.
Good luck! 🙂