Simple solution: Twilight should time travel and bring Fluttershy to the mirrorpool, copy her, put orignal Shy in a sleep spell until the morning after they do kill Flutterbat, then bring Copyshy to her house and put a spell on her that makes her believe shes fluttershy. This explain why the vampire fruitbats didnt respond to her the first time and it wont mess up the timeling