I see it like ImaginaryHuman does. I'd like to add you can place other points of detection in there as well. For instance, at the end of the area before the boss, the flip occurs. You could make it like that so that when you are at the end of the level and doing the pass into the boss chamber its set to always flip regardless of the direction. Use this with ImaginaryHuman's ideas, and I think you've got it.