Good day, nbailey0669. Yes, you can absolutely delete a manually recorded tax payment in QuickBooks Online and process it electronically.
Before you proceed, make sure the original payment was not sent and processed by the CRA or withdrawn from your bank to avoid double payment.
Once confirmed, follow these steps on how to delete the transaction:
- Go to the Tax menu and proceed to the Payroll tax tab.
- Click Payment history, then look for the tax payment you want to delete.
- Choose Delete payment.
- Select Yes, delete to confirm.

After that, process the payment electronically by following the steps in this article: Pay and file payroll taxes and forms electronically in QuickBooks Online Payroll.
If it's a sales tax payment, you can follow the steps in this article instead: Delete a sales tax payment in QuickBooks Online.
The Community is open all the time just in case you have more questions for us.