If the canopy was attached with PVA a.k.a. 'white glue' (or one of its near-relatives), then it should remove quite easily with little risk of damage to the clear parts themselves. It would probably simply 'pop' off with minimal pressure applied -- though, as you indicate, slicing the glue joint with a scalpel or #11 blade would be neater and give less chance of chipping where paint lies over a (possibly) irregular glue application.
If you're worried about possibly marring the clear parts with an errant blade, it would be simple enough to lay down strips of masking tape...which would also provide a straightedge 'guide' to cut against.
BTW, your paint job looks quite good!
Cheers