This story is a sequel to Things Change
When in the past Twilight had pondered the possibility of reforming Queen Chrysalis, she'd always thought about it in a hopeful way, imagining all the good things that would come from bringing her to the good side of things. The reformation process had certainly not gone the way she'd expected it to, but now Chrysalis was finally one of them, someone she could call a friend, willing to come with her and learn from her.
A creature strong enough to overpower Celestia, with no memory of her time as an evil shape-shifting love-stealing queen, with no knowledge of how to properly interact with others, and with a very poor understanding of how to treat personal space when meeting someone new. Maybe inviting her to stay in the castle in Ponyville had not been the best of decisions.