FWIW, I folded it down at the 2011 Moab Zukfari (different Samurai).
I really don't trust the flimsy buckle strap that comes with the kit though and I use a rachet strap to hold the windshield down (anchored at the grab bar and bumper). That way it doesn't bounce on the hood and there isn't any chance of the buckle breaking and/or the hood or windshield to come flying up.