When you amend a return, the data resets back to $0 so a payment showing is the amount of the previously issued refund that you will be repaying. The return won't reject for lack of attached payment, so that's a separate issue for us to troubleshoot.
Was is the rejection error code/message that you receive when you attempt to amend?
Also, does your notice request that you amend your return? If not, it is better to follow the instructions in the letter than to amend the return.
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