I'm going to let Star Trek sort this one out for you (lol):
"If we look at this from the perspective of there once being an original timeline, which is altered by the time travel, this obviously makes no sense since John Connor would have a different father in the original timeline, and would grow up to be a different man as a result. You can't just switch fathers and still give birth to the same person."
From memory alpha:
"Both Kathryn Janeway and B'Elanna Torres knew the "finer points" of temporal mechanics, which included understanding one of the more difficult concepts of the field to grasp, which was that "sometimes effect can precede cause" and that "a reaction can be observed before the action which initiated it." (VOY: "Parallax")"