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Best is to prepare the amendment (1040X - on paper) and keep a copy for your mortgage lender. The lender will be able to see the mortgage interest you want to report, and use the income as a qualifying factor.
Send it to IRS, certified mail, with a return receipt. The green receipt will serve as proof that IRS has the return, as many lenders are using IRS filed returns, not just the copy you might provide) to support your application. Since mailing your return in will take some time for IRS to receive and process, you can prove IRS has it, and that should remove that potential holdup.
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