No, he died during one of the first days of shooting on the loft set, while they were shooting the flashbacks. Everything else was already done, but just about all of the one-year-later loft scenes had to be reshot, that's why you almost never see his face in these sequences. You can see that when he enters the room, there's rain falling indoors, because he was mapped in from a shot outside in the alleyway. His face was also digitally mapped onto the shattered mirror while he's putting on the crow makeup, and they used a fragment of a previous rooftop shot for the first shot of the crow makeup revealed. Similarly, when Sarah comes up to the loft and meets him there, the voice is a fragment of her first meeting with him post-death (the "It can't rain all the time" scene) and the actor's a body double, that's why he's standing with his back to the window and you never see his face. One of the two doubles was a friend of Brandon's from the same dojo who could imitate his movements.

Uh. Did I ever mention I'm a total Crow geek, and that it was my first major obsession since I saw the movie in a deserted theatre on the third day of Christmas, 1994? I was 12 years old.