Beforehand, are you currently using direct deposit as your payment method? If so, we'll need to temporarily switch it to a paper check for an employee with a deleted paystub and then manually enter the paycheck. After that, you can update it back to direct deposit.
Here's how:
From your QuickBooks Online account, select Payroll at the left pane.
Select Employees.
Click on the employee's name from the list.
Tap on the pencil icon beside the Pay button.
Go to the number 7 section, then choose Paper check.
Hit Done.
For your visual reference, I've added screenshots below.
After that, let's enter the paycheck manually. I'll show you how:
Go to Payroll, then select Employees.
Choose Run Payroll.
If applicable, select your desired payroll schedule, then Continue.
Review the Pay period and Pay date.
Select the employees you'd like to pay and then click Preview payroll.
Check the QuickBooks Bank account to track your payroll.
Hit Preview payroll details or Submit payroll, then Close.