EasrsideAl brought up the salient point. Did you file jointly? The city used to require that you had to file the sane way as you file federally.

If so, you might consider filing an amended return showing your total income and then reducing it commensurate for the amount of time it was earned in the city [[supported by your records). When I was headquartered in the city, I traveled about 25-30% of the time, I kept track of all those days and then reflected the adjusted amount on my tax return [[I also always under withheld, so I would owe at year end and not be sent to that mystical world of expecting a refund).