Yeah I dont get what you mean with the color swapping either.

http://i.imgur.com/RLL7yLJ.png

Needs elaborate though.
AoNinger looks a bit feminine in this shot, so I guess this is Fuuka, some sort of ninja trick that they'll use later, which is similar to Change Lines in ToQGer. However the suit is not like women version so maybe I was over-sensitive.

I think that's just a weird angle. We would've known by now, if the Ninjas could color swap. If anything, it's a one time ninja trick like the many we saw in ep 1.