Yes. That's what my answer explains. You will input the mistakenly withheld resident taxes just like it is entered on your W-2 (and you will need to do 2 separate lines for the local tax, one for NYC and one for Yonkers), and these withholdings are added to your NYS taxes withheld. Once the system calculates your NYC/Yonkers tax (of zero), these extra withholdings get included in your New York refund.
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