No, from the information you've given, your federal return has been changed after you filed but before you selected "amend" so your federal return won't amend properly. The IRS will need to see the change from your original return to your amended return. Since your refund changed, once the Form 1040-X Amended Return is ready, you'll need to go back into TurboTax and remove the 1099 form from your return, then select amend and enter the 1099 form.
- Note: You won't have to amend your state return since you included the 1099 form on your state return.
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