My husband was stationed at Fort Drum, NY since November 2015 as active duty military, we both have lived in NY since then. I qualified for in-state tuition and NYS education funding because of his military status. In 2017, I got a part-time job. We have filed "married filing jointly" since we got married in 2015 in PA because that is my husbands home of record (we were both PA residents before he joined the military) and after I got a job I filed as a non-resident of NY. My car registration, voter registration, license, address, auto loan, etc are in NY since 2015. This January 2019, my husband retired from the army but we remained in NY. I transferred to a 4-year school and the school questioned my residency since I filed as a non-resident of NY. I have finished my return for 2018 but I have yet to file it as the residency director gave me the impression that if I did not file as a resident, I will not qualify for in-state tuition.
Also, I tried changing our return to reflect NYS residency and our taxes went from owing $9 to owing over $800 because it changed my husbands from PA to NY as well.
Is the best/cheapest option to file as "married filing separately" and for me to file in NY and him in PA, or do I still qualify for in-state tuition if I file as a non-resident of NY?