The metahuman situation was quite different in the Flashpoint timeline, so it’s not exactly clear how Mystery Girl would have traveled back into another timeline’s past events, but where there is a speedster (Wally) and a Cisco (billionaire jerk or not), there is a way.
So what if the Flashpoint timeline remained unstable and got as horrible for everyone else as it was for Barry, leading to Sara’s parents John and Lyla getting killed for one reason or another, leaving Sara to grow up miserable, afraid and in need of revenge.