Legal Question in Tax Law in New York

The answer is yes, you can always file an amended return, but it has a small risk while you are being audited. Unless you know that you missed something that should have been reported, by filing the amended return you might be exposed to additional issues. For example, if there was a questionable deduction in both years, that you are correcting and this might not be required, the auditor has the right to go back and forward on the same adjustment. So, unless you are filing the amended return to report something like previously unreported income, I would suggest not filing until the audit is completed.