I've got some ideas on how to handle your 1099s in QuickBooks, @mkahak.
Let me present two scenarios based on the information you've provided. First, you can unselect the expense accounts or make other changes if you haven't submitted your 1099s yet.
Here's how:
Go to the Payroll menu, and then choose the Contractors tab.
Click Prepare 1099s, and then Continue your 1099s.
Make the changes needed.
Select Finish Preparing 1099s.
If you've already submitted the form, you'll need to work directly with the IRS to make a manual amendment. Then, you'll have to provide the corrected return to the recipient or contractor yourself.