Hello Johnny!
So to say you can repair them like the real thing - by polishing - and then later like the modellers do it - by future dipping. Polishing canopies is best done with a multi-grade nail polishing file that you can buy at most stores where they sell even the basic nail supplies. If you buy one that has a core made of soft foam, you can cut it to smaller pieces to get into tight spots if you must. You can skip the roughest "phase" - on some files they are just too rough. The smoothest pad is around 5000 grade, so you can polish the "glass" pretty well. After that you might want to put the part in a glass of Future-like product, take it out and let dry for about 24 hours under glass, to make sure no dust will sit on it while it dries. This way the transparent part gets extra shiny and extra clear, and additionally it's protected against fogging should you want to use super-glue around it.
Hope it helps, have a nice day
Paweł