The penalty is not a part of your tax calculation, it simply gets added to the tax that you owe. Since the amended return only accounts for your tax and payments and credits against the tax, it does not address the penalty situation.
However, if you include the form 2210 with your amended return along with a note to refund your penalty, the IRS should reduce your payment due by the amount of the penalty. So, just write a letter explaining what you are doing and mail the amended return without a payment and the IRS should process a refund for you.
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