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I'm so glad to hear you're able to restore the correct company file, Alpinewood. Now that your file is back, I'm eager to help with your questions about payroll.
You also mentioned that the paychecks were recreated as regular transactions. As long as the Use Direct Deposit box was unchecked, the employees will not be paid twice.
Aside from that, you also need to edit the paychecks and include a Direct Deposit offset item. Please note that missing direct deposit transactions need to be recreated with zero net pay. This is because the total amount of all paychecks should be reflected in the direct deposit liability check. It'll help balance your check register and make sure your employees aren't paid twice.
Please see these articles for more details: Recreate a Missing or Voided Direct Deposit Paycheck in QuickBooks Desktop Payroll.
However, I would still recommend reaching out to our Payroll Support Team about this. They can take a look at your payroll account and make sure that everything is sorted out.
Here's an article on how to get their contact details: Contact Payroll Support.
Let me also share these articles in case you might need them when using the Direct Deposit feature in the program:
Don't hesitate to visit us again if you have questions when paying your employees and when restoring the missing payroll data, Alpinewood. Consider me your ongoing resource as you make sure everything is sorted out and recreated.
