Them being sent to an alternate reality by Madara or a mass genjutsu by Madara would make the most sense. If it's the later Sakura is still herself and is aware of the genjutsu because of the ability Kishimoto has shown Sakura has- in part 2 even resistant to Uchiha level genjutsu. (maybe this will be the Sakura arc that Kishimoto promised but may have run out of time to put in the manga) If the story is about Sakura knowing the situation is wrong and she has to make the heartbreaking situation of freeing Naruto from a genjutsu where he has loving parents- whoa... that will be intense. (but right up Kishimoto's alley....)
I do hope so this will be Sakura's big role in a Naruto movie.