@isaacamick --
Here are NY's appeal instructions:
https://www.tax.ny.gov/tra/disagree.htm
Looks like you can't file an appeal until you receive a notice from NY that you're being assessed a penalty. The notice (if you get one) should contain appeal instructions. Then you can tell them exactly what happened.
**Answers are correct to the best of my ability but do not constitute tax or legal advice.
