We could assume that the pony with the cookie cutie mark has always been the same one and keep Sugar Cookie and the alias Pizzelle for her. Maybe she wore her hair differently in Wonderbolts Academy, maybe it's an animation error. That way we get two ponies with similar looks.
We could also assume that the pony in Wonderbolts Academy is yet another pony. Since the one with the bangs is named Pizzelle in the Wonderbolts Academy Handbook, only the one with the curls in Wonderbolts Academy would keep the name Sugar Cookie, the one with the bangs would keep the name Pizzelle which would be un-aliased. That way we get three ponies with similar looks, two of whom are shown as Wonderbolts trainees on screen, but never at the same time. But then we'd have to, for example, split Orion into three ponies, too: fancy Earth pony, fancy unicorn, spiky unicorn.
I'm in favour of the former solution, but I'm not the one to decide.