While the amended return ( form 1040 ) is like a new return with the updated facts, the form 1040-X is a reconciliation i.e. it assumes that the original return has been processed and refunds issued or dues have been paid. This how IRS sees it.
Given the above I do not understand your statement
"overpayment from original tax form which has not and will not be paid"
Overpayment , from IRS perspective is a refund issued to you -- so why would it not be paid to you, if the original return has been processed ?
Please explain
