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Hi. What the IRS said they don't have a record of, the original 1040 filed via turbo tax (I assume you e-filed) or the 1040X? It is not unusual that IRS "lost" mailed in returns. If you have a proof of mailing your return (certified or registered mail receipt) they might be able to locate it. If not mail another 1040x (same as the first one) via registered or certified mail. If, in meanwhile, IRS receives the first one, they will disregard the second one. Since they owe you don't have to worry about any penalties or late fees.