It depends on the source of your New York and New Jersey wages. The duplicate wage box is for wages from the same W-2.
NJ taxes income differently from NY so TurboTax allows you to remove duplicate wages. For example, New Jersey does not allow you to exclude from wages amounts contributed to deferred compensation and retirement plans, other than 401(k) Plans so the NY and NJ taxable wages will be different from the same employer.
If your NJ wages are from January to September and the NY wage if from October to December then do not remove NY wages because they are from different employers.
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