Hard to tell without seeing it, but -------------- I would probably use a very sharp wood chisel (upside down) to carefully pry up the run, and then polish out the fingerprints and remainder of the run, and any damage the chisel inflicted. I suspect you may get lucky and the run will pop off reasonably easy. Be careful to not apply too much pressure to the plexi--------you do not want to crack it.
Use tape to cushion the undamaged areas if you use a chisel or similar to pry up the runs.
If you have any scrap canopy left over, do some testing. Or any other scrap plexi.
What you have going for you is that the epoxy does not hold really well to a surface that has not been scratched with sandpaper first.
Other plan would be to mask off the good plexi and sand out the run. Then polish out the last bit of the run, should be the thickness of the masking tape.
Whatever you do, would best to test on scrap first, and go slow and easy.
Good luck.