I chose to take out the nydus canals instead of air... I went back and beat shatter the sky thinking I would then have the choice of playing "All In" either with nydus, or air............................................. do I actually have to play the entire campaign all over again to switch?
Either play the campaign again, or load a save from a time before you made that choice. This is why I always make a separate save when I'm about to play one of the choice missions.