I sincerely doubt it. Prometheus is a part of the Alien franchise of movies. But frankly I don't know much about the Xenu story, other than what I read online.
I do know that Scientology's spiritual counseling technology is pretty powerful stuff. I've had hundreds of hours of it, myself. And it's a blast. A vast increase in awareness. Just to give you a small example. Senior year of high school, I was struggling with my English Literature class because of tons of homework and lots of memorization. I had mostly A's in high school, but this was my first ever D. I worried about the mid-terms and my parents paid for some spiritual counseling. It was my first and I didn't understand what was going on, but the results were stunning. In the week before the mid-terms, we reviewed materials in class and I soaked them up like the proverbial sponge. I got the only A in English Lit class.
Scientology holds that we are not our bodies, but most religions do, too.
Scientology also holds that our true selves (spirit, soul, Holy Ghost or what they call "thetan") has had many incarnations -- past lives.
Surprisingly, for many Christians, Christianity and Judaism also include reincarnation, though not traditionally.
As a Christian, I have to thank Scientology for helping me be a far better Christian. But I also thank my studies in Buddhism, too -- especially with Rinpoche Gyaltsen, a Tibetan Buddhist monk I met in Los Angeles.
I don't doubt that there may be some influences on movies from Scientology, because there are so many Scientologists in Hollywood. And I had worked with some of them when I was an artist in Hollywood back in the 70s, 80s and 90s.