It's not clear to me how you are actually preparing the Amended NC tax return.
You are supposed to "start" with tax return you originally filed in the software (without the sales/Use tax entries) ....then hit the "Amend" selection and proceed to enter/change whatever needs to be changed in the regular interview.
The tax software then prepares a new D-400, with the "Amended Return" box checked in the upper-center of the form, and all the old numbers, plus any changed ones will be shown on the whole form in the appropriate lines.
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Any additional taxes due are not paid thru the "app" in any way in this situation, since the NC amended forms have to be mailed in by you at the US Post Office. So any additional tax due is paid with a check sent with the forms, or a Direct Debit arranged on the NC tax payment website.
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____________*Answers are correct to the best of my knowledge when posted, but should not be considered to be legal or official tax advice.*
