The rejection came from the IRS, so this means the database for the IRS was likely updated between when you originally filed and now. Although they have your other form, the fact that you are amending a return for a deceased person may be causing a glitch in their system with accepting it.
You will need to print and mail the amended return. If you select print and mail, you will have the instructions and address as to where to mail the 1040X.
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