Although the flaps were normally in the neutral (up) position on the ground, those pics I've seen of them deployed show bare metal along the hinge line.
You can possibly save the canopy if you polish it with 'T-Cut' (Auto body colour restorer) or metal polish. Depending on how 'deep' the damage is, it may need gentle sanding first, using very fine wet n' dry. Otherwise, it's time for a vac-form replacement from squadron or similar.