If you choose to mail in the Missouri amendment, you will not need to efile or mail in a Federal return for starters. It might be simpler to mail in the Missouri amendment.
As far as amending the original return is concerned, you claimed a refund and your "original column" should state that. However, there also should be an entry for refund actually received, if different. Look for that entry and put the amount you actually received, $0 if you received nothing. There also should be an entry for amount paid. This will also be $0 unless Missouri sent you a bill and you paid it. This reporting should square away what the state should refund you, along with the proper documentation.
And it might actually be necessary to amend. Look at the letter Missouri sent you. You might be able to submit the proof that their calculations are incorrect, and then they can fix it without amending. If in doubt, contact Audit Services, and they can help you understand your letter. See this link for more information: TurboTax Audit Support Center
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