If you mean that you've set up a non-profit vendor for 1099 tracking, you can correct this by making the vendor inactive. Here's how:
In your QBO account, go to Expenses.
Select Vendors.
From the Action column, select the drop-down arrow.
Choose Make inactive.
On the other hand, if you mean you mistakenly filed a 1099 form for a non-profit vendor manually or electronically, you will need to submit an amendment form to the IRS to correct the error. I suggest contacting the IRS for further guidance on cancelling the form. Additionally, you should also communicate with your non-profit vendor and explain the situation to them.
Furthermore, you can also submit amended 1099 forms in QBO. However, we don't have official instructions for this yet. You can check back the instructions through this article at a later time: Correct or change 1099s in QuickBooks.
We're always here in the Community should you have updates on the filed 1099 for your non-profit vendor. Take care.