Sorry, but you know you owe the other half of the SE taxes that were delayed in collection. You got an IRS notice for the first payment and now it notice for the second payment so you can either make the second payment timely or it will come out of your refund next year the same way it did this year plus penalties and interest for the late payment. Arguing about it now will do you no good. These were taxes you would have owed two years ago but we're allowed to be extended and paid in two installments. Whether you wanted to do it or not it is now done and there's nothing else you can do about it.
