Your confusion ends here, @Kimberly74.
Allow me to fill you in on everything about changing the vendor name connected to the transactions.
The possible reason why your newly created vendor had a credit is that you directly change the vendor name on the bill payment. When you change a vendor to the bill payment, this will lead to the original vendor having an open bill. In that case, you'll need to apply the checks to the open bill transaction of the original vendor. Then, consider deleting the bill payment associated with the new vendor to get rid of the credit.
Most importantly, I still recommend checking with your accountant for more guidance. They may add suggestions based on what's more suitable for your business and to your books.
Once you already fix the vendor balances and the reconciliation, you can now proceed with filing 1099s in QuickBooks Desktop. For more guidance, feel free to check out this article: Create and file 1099s with QuickBooks Desktop.
Please let me know if you need clarification about this, or there's anything else I can do for you. I'll be standing by for your response.