I first heard about the missing windows at LetsRoll Forums. Here is some photographic evidence to support their hypothesis:
This is a closeup of the right corner of the gash. Notice the windows – or absence of them.
Whatever it is it is attached to the frame.
What is this material? It looks like some sort of paper or plastic sheeting. It isn’t glass, and there isn’t any broken glass visible. Were these floors occupied? Were any of the floors around the impact zone occupied?
Here’s a great shot showing what appears to be screens used to mask the missing windows: