Do have one more search.
Sam and jack meet when she's in high school? just graduated? she lies about her age, get's pregnant. before she can tell him- he marries sara (who is also pregnant.).
Jacob adopts the baby and she is raised as sam's full-blooded sister. sam goes to the afacademy, yadda yadda.
when she joins sg1 - jack gets to know the little girl, but not that she's really his daughter. He and sara are separated/divorced and it's ugly.
it is NOT jen camp's "Through the Years",
or Ruth M. King's "Rockets and Shooting Stars".
pretty sure it was on sj-always&forever, but I thought it was moved to AO3.