As Draven first enters the apartment after digging himself out of his grave: footage of Lee walking through an alley in the rain was digitally composited by (ILM) into the scene where he walks through the doorway. Computer technology added drops of water to the door frame and around him to make the water on his back not seem out of place.
The scenes of Draven falling from the window was made by digitally compositing Lee's face (complete with simulated blood) on to a body double.
The scene where Draven puts on his make-up was filmed using a double. The face in the smashed mirror was indeed computer-augmented by superimposing Brandon's face on to a body double. This and several other of the post-accident 'enhancements' are seen on the the show Movie Magic a series seen on the Discovery Channel.
The image of Draven walking towards the window with the crow on his shoulder was cut from another scene, with a computer-generated crow added.
When Sarah visits the apartment, we never see Draven's face as it is a body double.
Scenes featuring Michael Berryman the "Skull Cowboy" were cut. When Eric is dead, he is visited by the skeletal character. In early scenes, he merely tells Eric to "Follow the crow", but later he explains why Draven is "alive", namely, to kill the bad guys and reunite with Shelly. A problem: "You work for the living and you bleed." After Sarah is kidnapped, the Skull Cowboy appears to Eric for the final time and tells him that it is time to return to the land of the dead and give up the concerns of the living, Eric refuses, and Skull Cowboy tells him. "Then choose and be damned!!!" This is why Eric gets hurt at the end, not because of the crow being shot. (This one was previously located under scenes cut unrelated to Lee's death, but Jim Timko informed that they were in fact cut precisely because of it. Apparently, O'Barr felt it would be in poor taste to leave them.)
These scenes were edited or cut, though perhaps not as a result of Lee's death:
A scene was cut in which T-Bird and his gang go and blow up an Arcade place and then victimize a young girl. Eric finds her as he stumbles to his home, reminding him of what had happened to him and Shelly. Eric gets clues as to who they were and what they did through the girl because he has his first flashbacks by touching her, as he does many times in the rest of the movie.
A scene was written in which Eric ties a spent shell in his hair after killing an enemy, but it did not appear in the film. However, you can see the shell in his hair if you look close enough. This symbolism was portrayed often in the graphic novel.
When Eric helps Darla he opens himself up to injury (remember the warning of the Skull Cowboy). Funboy gets out of the bathtub, inhales a large amount of cocaine, grabs the razor that Darla had dropped from attacking Eric. Because of him dealing with Darla his wounds did not heal. The scene with Eric pulling Funboy from the bathtub was a body double.
The scene of Skank getting smokes and road beers at a convenient store was edited. The shop is robbed by two youths, who shoot Skank in his leg as he runs out after seeing T-Bird take off in his car. That would mean the limp that he had after the car chase was due more to the bullet wound than to the hit and run and the car accident.