State tax filing

@maglib With all due respect, I am one of the leading experts in this field. The size of a firm, does not validate the expertise of its partners. 

Section 132.18(a), the part of the law that covers the convenience rule, has not changed since Matter of Hayes. The New York State withholding guidelines, as of todays date, tell employers they do not need to withhold on employees who perform no services in the state of New York. 

In your case - it sounds like there were potentially one of two problems. There were days he actually worked in NYS or he could not prove that all of the days were worked out of the State given the proximity to New Jersey. 

Matter of Zelinsky is a recent court case on telecommuting in New York. Professor Zelinsky worked in NYS for a portion of the year (January-March 2020), his facts are not the same. There is nothing you are going to tell me that I don't know. I have represented ultra high net worth clients in over a thousand New York State tax audits. I used to be a New York State tax auditor myself. I write about the cases and follow changes in every state in the country. 

I've handled at least a dozen cases last year, citing the Matter of Hayes, with zero New York workdays, and I have won all of them. 

If this individual you speak of is a W-2 employee, truly works no days in NYS, and only commutes to Long Island for personal reasons, they are paying NYS taxes they should not be.  Did anyone attempt to prove that this individual did not work in NYS by using their cell phone records to track their physical presence and support that he was in fact only transiting through to Long Island and not working in the state? Did they request swipe card records from the building supporting he didn't go in? 

My advice stands. If OP did not work in NYS, their wages are not taxable in NYS. 

You can Google me and find me on LinkedIn. Feel free to call to me and fill me in on all of your facts. If what you say is true, and this person didn't work in NYS at all - happy to take it on as a contingency and get you your money back. I'm very good at what I do.