All you need to do is invent another branch on the tree - as you could do for any "new" creature (whether living or fossilized).
Sure, we can just group your flying pigs with the crocoduck. However, that "branch" would be stuck out all on its own with no connection to the "Tree of Life". That is because of their common characteristic of being something really stupid that had sprung forth fully formed from a creationist's ignorant imagination.
We didn't didn't know there were mammals that grew wings out their ribs, but now we do, so, we just add a branch to the base of the mammal branch.
Except no such critter exists. Nor do we know of any mammals who "grew wings out their ribs". Your ignorant musings are completely divorced from reality and from common sense.