Hey, sorry, I just realized I never responded to it.
My opinion...
Alternating is not going to 'break' anything. However, I think the game plays at its worst a) in year 1 of a franchise and b) the first game after making a slider/difficulty change. If you're in Year 1, I'd keep going.
But regardless, I think constantly changing back and forth (or being one of those that suggests doing a "slider reset" prior to each game) is doing one's self a disservice. You'll probably see more bad animations (warping, clipping, and so on) by taking this approach. It doesn't so much alter the gameplay as much as it de-syncs it.