What if a flag is thrown during a called-back play?

Say Team A runs the ball and fumbles it. Team B picks it up and runs for a touchdown. During the runback Team A commits a foul on Team B (say an unnecessary conduct flag). However, the play is reviewed and it is deemed that Team A's player was down before he fumbled it so they keep the ball.....does the flag that was called on them after the ball was 'fumbled' still count against them? Thanks for any answers