Are you saying the employer withheld it to the wrong state?  If that's an administrative error, your client should ask the employer to issue a W-2C instead in the first instance.

Otherwise, report the wages as shown on the W-2 - you can't just "change the wages to 0" when a different amount is reported on the W-2.  Assuming your client is an NR of NYS and had no NY workdays, complete IT-203-B with all the day counts and it should then allocate $0 to IT-203, Line 1, for New York State amount.  This way, IT-203 will still show the SIT for NY and it will not trigger any critical diagnostic.