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"
submit the corrected pages of the return, according to the instructions you got. it sounds like just one page is incorrect.
make sure you are mailing back to the address specified in your rejection letter.