I want to ensure that you'll be able to delete your employees' paychecks successfully.
If you've processed a direct deposit paycheck, deleting the paychecks may vary from the time it was created. Deleting a direct deposit paycheck should be done before 5 PM (PST) and to banking days before the check date.
To verify the reason behind the error that you received, I'd suggest reaching out to our Customer Care Team. They have the tools to check on your transactions and isolate this matter for you.
Lastly, I've added here some resources that you can visit for more details about deleting a paycheck in QuickBooks Online: