You don't need to worry about the EIN on the 1099. It is for a deceased person and the amount is not significant. It will go unnoticed by the IRS. And if it were, you would be able to show that it was reported on the amended Form 1041. And if your mother were alive, the amount, $5,000 would be below the filing threshold, so they would expect a return to be filed just for that. Just report the interest on the 1041 as if you didn't receive a 1099.
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