I don't think the Bolton's will care that Arya isn't really Arya. So long as they have someone who looks like Arya, and keeps saying "I'm Arya Stark" like a trained parrot, and while there are no Stark's around to contradict her claim to Winterfell, then what does it matter? The Bolton's will have a claim to Winterfell that is, for all intents and purposes, unassailable. With Sansa disappeared to the Eyrie, Bran and Rickon presumed dead, and Robb being...well you know, there isn't anyone to contest the claim. It's all about appearences being one thing and the reality being something much different.