Damaged Canopy
Man, I feel your pain. I've spent a couple of weeks, replacing my canopy. It cracked on a very cold day, in front of Jay's RV Central. At least I got several years of flying out of it.
If your Lexan has melted, and there in an low spot in the surface, it will be weakened there, and can not be polished out. Your option will be to fly it as is with this optical defect, or replace it. Removing the Sikaflex might damage the frame's powercoat finish, and may need repainting prior to installing the new glass.
The Doll has been flying for nearly twelve years, so I'm using this experience to make some repairs. I welded up and re-drilled a few of the oversized #30 holes in the canopy frame. I have corrected a building error by extending the canopy skirt forward to match the canopy glass along the front edge. When the weather improves, the frame and skirt with get fresh paint. This repair will take me longer then the original build time.
Good luck with whatever you decide to do.