Update your answer to the question about receiving the 1099-MISC to "no" for next year. This is a software question designed to help ensure the proper treatment of the 1099. Your situation doesn't quite fit the typical scenarios that the software is testing for here, so that change should move the answer to the right place on the tax return and remove the self-employment tax.
This answer isn't an IRS question and doesn't get transferred to your tax return so it won't result in any false report on your return.
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