yeah i had body work done on the passenger side of my car. I was T-boned by a truck. But i had problems with the front window getting stuck..
Well the problem that they found was that the guide'track' (on the front and rear of window frame) was pinched on on the rear.. So when the window was going up it was sticking and scraping.
You can just take the inner door trim and foam insulation layer off and take a look in the door frame to see if the track is pinched or need 2b greased. But it might be the track being pinched causing the scraping sound.. the glass goes in at a slight angle when you put it back in the door. It might have bent the track a bit.. Hope this helps..