It should be accounted for on your NYS return. The reconciliation of NYC tax is included as part of your state filing. As a NYC nonresident, you are not liable for the tax even though you were with an NYC employer. However, you need to make sure you claim this on your tax return. You will see a section on the NY State return that asks if you are a NYC resident, and you will select no. This will allow NY State to apply your NYC withholdings as part of your NYS refund.
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