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Amended 1040SR, 1040-X and Form 1040-V

I used TurboTax for my 2020 tax submittal, and then used their amended return process to add a 1099-INT and K-1 beneficiary forms.  I had a tax overpayment on my original return of $10,204 which I planned to apply to 2021 estimated payments.   The amended return 1040-X summary showed a total tax increase from $77,796 to $82,792 (difference of $4,996). I followed the instructions and sent a check to the IRS for $4,996 with a voucher (Form 1040-V).  The amended return 1040-SR revised my 2020 tax overpayment from $10,204 to $5,208 (difference = $4,996).  Since the $4,996 in new taxes was taken from my 2020 payments on the amended 1040-SR, was it correct to also send a check for $4,996?

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Amended 1040SR, 1040-X and Form 1040-V

You submit your taxes with TurboTax and then receive some additional income statements.  You select amend your taxes with TurboTax to add the additional income, and you follow the process.  The resulting amended return instructions and required steps direct you to mail a balance due to the IRS for the new taxes from the additional income, and the amended return shows an overpayment after the new required taxes are deducted.  I must be missing something pretty fundamental because it seems that with the amended return process, I wound up having the new taxes deducted from my taxes paid, and I had to pay again for the new taxes with a check.  Why a check when the new taxes in the resulting amended return are deducted from taxes already paid?

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