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State tax filing
On the New York return, there is a section that deals with your New York City residency specifically. Put the dates in that section. Also, make sure you mark in the New York state main return the amount of income that was earned as a nonresident as compared to the period that you earned as a resident.
You will be filing Form IT-203, for a part-year/nonresident return. As you state, all of your income is still taxable to New York state, but the portion of the income that is nonresident income is not taxable to New York City, since they only tax residents of NYC. Once it is determined how much income is taxable to NYC, and the tax calculated, what was withheld beyond the end of your NYC residency should be refunded. It won't be the entire amount of the NYC tax withheld, but it will be at least the portion of it that was withheld after no longer being a NYC resident.
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