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Why does the IRS say not to file 1099-MISC NEC payments with other payments after January 31st?

If any of your Forms 1099-MISC reporting NEC will be filed after January 31, 2020, file them in a separate transmission from your Forms 1099-MISC without NEC (due March 31, 2019). Filers should anticipate that if transmissions sent after January 31, 2020, include both Forms 1099-MISC reporting NEC and Forms 1099-MISC that do not report NEC in a single transmission (on paper with a single Form 1096 or electronically through FIRE with a single payer “A” record), the IRS will treat every form in the single transmission as if it is subject to the section 6721 penalty for failure to file by January 31, 2020. The IRS may send you a Notice 972CG, A Penalty Is Proposed for Your Information Returns, to which you may respond and clarify the content of the submission, indicating the number of Forms 1099-MISC that did not report NEC.

For additional information see the 2019 Instructions for Form 1099-MISC