It depends on how you want the duplicate payroll to be treated in QuickBooks Online, contact117.
Since printed paychecks have been distributed and the Direct Deposit can no longer be cancelled, you'll need to inform your employees about the duplicate payroll. Then, discuss with them or have an internal agreement whether to treat it as an advance payment or deduct it on the next paycheck.
You can follow these steps to create a deduction item in case you decide to have them pay it back:
- Go to the Payroll or Workers menu and proceed to the Employees tab.
- Click the name of the employee and click the Edit or Pencil icon next to Pay.
- Scroll-down to the Deductions section and click Add a new deduction.
- Select Deduction/contribution in the first drop-down list, then New deduction/contribution in the second one.
- Select Other deductions in the third line and click Cash Advance Repayment in the drop-down list for Type.
- Click the drop-down list for Amount per pay period and select amount, then enter the amount of the deduction in the field next to it.
- Click OK.
Once done, the deduction will automatically show up in the next paycheck. You'll also want to reach out to your accountant for additional advice on this matter.
Feel free to check out this article as well on how to run a report if you want to review the payroll transactions in QBO: Run Payroll Reports.
I'd be glad to get back here if you have any other questions.