After you file

Hi-this is our exact situation! Spouse works for NY parent company but is based in Illinois so we pay income tax here-they accidentally did NY tax for a couple of months and we are cleaning up their mistake. I followed your advice-thank you so much by the way-but when I go to transmit, it tells me that NY will reject my return since I put 0% for the income earned there.  Can you advise? I can't submit anything unless I correct this.

Is submitting Illinois and Feds an option and then just mailing the NY?