I only filed 1099-MISC forms for rent. I never took their "suggestion" that I use the 1099-NEC form since it did not apply. I don't know if I follow what you actually did. Did you file 1099-NEC forms after the MISC forms were rejected that were not Non Employee Compensation? You may need to refile the 1099-NEC and mark them as "corrected" with 0.00's. This whole rejection thing has caused people so much trouble and uncertainty when we were doing things the right way.
