Hi
I would recommend going to Setup>>Preferences>>Security Tab and enabling the preference "Transactions can't be changed they must be reversed". This will allow you to go to that relevant transaction and select Edit>>Reverse transaction. By doing so you would be able to generate a reversal transaction (.e. money coming back into the business) to which you can match to your deposit bank feed transaction.
Once that reversal has been recorded you would go through and record the original transaction again i.e. go through the Payroll>>Process Payroll or Spend Money process again to record the money being correctly paid to the employee.
Do let us know how you get on and if you require further assistance.