If you entered your carryover loss in the Property Profile section of Rentals on your Federal return, it would be included in Schedule E calculations, on Line 22. Since the loss is included in the Federal AGI that carries over to New York, you don't need to make an adjustment for rental income in NY as a non-resident, as you mentioned.
Because TurboTax will include Schedule E in your NY Efile, they will have the info regarding the carryover loss amount each year.
@nj30
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