NY does their dissolution a little different than other states. You file your final return and then you receive a letter from NY where you must respond. If you received that notice and responded, then you won't have to file again. It might still be active because of the failure file prior year forms.
Based on what you wrote, their correspondence is regarding a 2016 issue. You forgot to include form CT-3-M. You have to fill that out and mail it or go back to the tax program that you used to prepare the return and add it.
Did they mention the year the franchise tax return was missing? That would be CT-3-S.
