If I understand your question, you filed Forms 1099-NEC to S-Corporations when it is not required. If this is the case, then you can correct these forms by sending the corrected forms to the IRS (and state if applicable) by putting zero in the income box reported and marking the 'CORRECTED' check box at the top. Also include the Form 1096 transmittal.
Do make sure to report the total income for your S-Corporation and just retain the 1099-NEC you received in your tax files.
Instructions Form 1099-NEC and 1099-MISC:
Some payments do not have to be reported on Form 1099-NEC, although they may be taxable to the recipient. Payments for which a Form 1099-NEC is not required include all of the following.
Generally, payments to a corporation (including a limited liability company (LLC) that is treated as a C or S corporation).
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