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Yes. If your employer is based in Arkansas, Connecticut, Delaware, Massachusetts, Nebraska, New York, or Pennsylvania, you must pay income taxes where your employer’s office is located. File the NY return first and MI will give you a tax credit for the tax you pay to NY. See Out-of-State Employers.
The income of a New York non-resident who never physically works in New York is not subject to New York taxation.
File NY Form 2104.1 with your employer:
https://www.tax.ny.gov/pdf/current_forms/it/it2104_1_fill_in.pdf
If NY taxes were incorrectly withheld, file a non-resident NY tax return on which you show the withholding, but allocate zero income to NY. This should result in a full refund.
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