Okay, I'm gonna go nuts here, trying to explain what I see here. I figure in the reality known as My little pony, nothing can stay terrible forever. Here's what would play out if Chrysalis actually managed to invade. Now, changelings feed off love, right? Violence cannot remain forever, or there's no love to feed on, so then she seeks to please the occupied peoples. Thus, she reluctantly places the two sisters back into power (along with her, she can't lose it.) With the day and night guard back in their rightful places, Chrysalis Needs her own guard. Stormy becomes one of the first knights in the regiment of change.