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You'll want to make sure that the accounts are properly mapped for both the 1099-MISC and 1099-NEC forms. Before doing so, please create a back up copy of your company file. This way, you can restore the backup data if you ever run into problems.
To correct the boxes, you can follow Step 4 in this article: Create and file 1099s with QuickBooks Desktop.
I'm also adding this link for more information: 1099 E-File: QuickBooks Desktop setup, troubleshooting, & FAQs.
I'll be around if you need more help with QuickBooks Desktop. Just leave a comment below and I'll get back to you as soon as possible.