Q. I'm wondering if I have to now pay to file in NJ and NC.
A. Yes.
The general rule is (it's not just NC): your report all your income on your home state return, even the income earned out of state. You file a non-resident state return for the state you worked in and pay tax to that state. Your home state will give you a credit, or partial credit, for what you paid the non-resident state. You will have to file a non resident NC state return and pay NC tax on the income earned there.. You will also file a NJ full year resident return and calculate tax on ALL your income. NJ will give you a credit, or partial credit, for the tax you pay NC. So, there will be little or no double taxation, but you have the cost and hassle of filing two state returns. Do the nonresident state return first.
You might want to ask you employer, why after 16 years, they thought this was needed. Chances are, they were getting some pressure from the NC tax people.
Technically, in this situation, the NC tax must be paid, but "nobody" does. See http://money.cnn.com/2013/06/28/pf/taxes/business-traveler-tax-threat/
