Go to Menus > Invoices
Find the Invoice for the chargeback
Click on the “Commission” button.
Click “Edit” and change the Commissionable Amount to a negative amount.(Do not make the % negative as well, as this will make the total a positive number)
Delete the Date Pd and Check #.
Click OK.
When you next go to pay the Rep’s commission, this invoice will show as a negative commission amount, and the deduction can be incorporated in the total amount paid.
You should probably enter a memo on the invoice referring to the original commission check, since using the above process will delete this data.