The Patriots would likely be fined, with the possibility of losing a draft pick or two if the league decides that it was a particularly egregious offense (which seems unlikely to me). They would not vacate the win and would still play in the Super Bowl.
"Well, evolution is a theory. It is also a fact. And facts and theories are different things, not rungs in a hierarchy of increasing certainty. Facts are the world's data. Theories are structures of ideas that explain and interpret facts. Facts don't go away when scientists debate rival theories to explain them. Einstein's theory of gravitation replaced Newton's in this century, but apples didn't suspend themselves in midair, pending the outcome. And humans evolved from ape- like ancestors whether they did so by Darwin's proposed mechanism or by some other yet to be discovered."
-Stephen Jay Gould
-Stephen Jay Gould