It depends on when the sale takes place. If you sell so that you will have used the home for at least two years within the five years before the sale, you will be able to take the exclusion. If it takes a long time to sell and you are no longer using the New York home as your residence, you may be out of luck.
On Form 1040X, you may file an amended return within a three-year period to claim a refund or correct a mistake made on an original or previously amended return.