Deleted Final Scene (Jezebel's transformation)
There were a number of filmed JL scenes that didn't make the final cut. Most of them were good, but only one of them was crucial: Jacob encountering Jezebel when returning to his ex-wife's apartment, and watching her transform into an image of Jacob himself.
In the director's commentary, Lynne said that including that scene would have been one disturbing horror too many for the film. I disagree - it would have tied all of the psychological threads of the film far more effectively than the ending that we got (Jacob ascending into heaven with his deceased son without any further wrestling with angels, demons, or himself).