"I finally managed to persuade Mary Jones, who was Whitney’s longtime assistant and probably knew her in her last years more than anybody, to talk [on-camera]," Macdonald, 50, told Vanity Fair Wednesday about the molestation allegations presented in the film.
"She talks about what Whitney felt and what effect it had on her. So we changed the whole cut at the very last minute. It was kind of a detective story to get that piece of information, which changed how I felt about Whitney and how I felt about the story," the filmmaker continued.
In the documentary, Jones recounted a conversation she had with Houston before her death.
"[The singer] looked at me and said, 'Mary, I was molested at a young age too. But it wasn’t by a man — it was a woman,'" recalled Jones. "She had tears in her eyes. She says, ‘Mommy don’t know the things we went through.’ I said, ‘Have you ever told your mother?’ She says, ‘No.’ I said, ‘Well, maybe you need to tell her.’ She said, ‘No, my mother would hurt somebody if I told her who it was.’ She just had tears rolling down her face, and I just hugged her. I said, ‘One day when you get the nerve, you need to tell your mother. It will lift the burden off you.'"
Also in "Whitney," out in theaters July 7, Houston's brother Gary revealed his own experience with molestation.
"Being a child — being seven, eight, nine years old — and being molested by a female family member of mine. My mother and father were gone a lot, so we stayed with a lot of different people ... four, five different families who took care of us," he said.
Macdonald told Vanity Fair that before he received confirmation of the allegations from family members, he had a suspicion that Houston had suffered abuse in some way.
"There was something very disturbed about her because she was never comfortable in her own skin," Macdonald told the magazine. "She seemed kind of asexual in a strange way. She was a beautiful woman, but she was never particularly sexy."
Representatives for Dionne Warwick and Cissy Houston did not immediately return ABC News' request for comment. A rep for Gary Houston had no comment.