We don’t know much about how Supergirl fits into the Flash film. Until now, there were no rumors that the character was going to appear in the Flash movie at all. While the main Supergirl in the comics has usually been Kara Zor-El, Superman’s cousin, that might not be the case here. We know that The Flash will explore the Multiverse. This is how Michael Keaton’s Batman is going to appear.
It’s quite possible that this Supergirl hails from a parallel world as well. She could be another version of Kara. But she could also be Lara Kent, the daughter of Superman and Wonder Woman. The possibilities are endless in the Multiverse!