When Henry is doing the autopsy on the heretofore unknown body, he states that "she has been exposed to an intense dose of radiation" implying that he knows that the body is female, and what happened.
In the very next scene, Carter says that they can rebuild their John Doe on a cellular level implying that they don't yet know that the body is female. That is because Henry knows who the body is and no one else does.
Jack goes back in time to fix the time line. He has to prevent Henry from doing what he does to change the time line. Henry knew back in the old time line that what he was about to do would change the time line and ultimately save the woman he loved because Henry had gone back in time first.