After living and working in nys for many years I moved in November 2009, how will it effect the monies owed to me from the 2009 tax return

You need to file a part-year resident return with NYS, covering your income and taxes withheld by NY while you were a resident there. If the state owes you a refund, they will send it to you.

You'll also file a part-year resident return for MS, to cover the time you lived there in 2009.