Hi there, missmissySEI.
In QuickBooks Desktop (QBDT), if the payment has been submitted to Intuit or already sent to the agency, there are no longer adjustments will be made. That means you are only canceling the payment, but the payroll tax calculations remain unchanged.
You'll want to recreate the replacement paycheck with zero net pay. This way, the total amount will be reflected in the direct deposit liability check. This will help balance your check register and ensure that your employees are not paid twice.
I'll share the article on how you can recreate a missing or voided direct deposit paycheck in QuickBooks Desktop Payroll for the detailed steps.
Don't hesitate again or click the Reply button below to post if you have any other concerns about voiding a paycheck in QBDT. I'm always here to help. Wishing you and your business continued success.