If the shortfall is exactly the discount amount and the customer has transferred in the period, the discount amount will be written into the "Discount" field in the "Incoming payments" module when receiving payments with bank statements.
In case of manual "Mark as paid", fill in the field manually. To do this, enter the actual amount in the field (the amount that the customer has paid). Then click on the discount icon. Then the difference amount will be automatically posted to the "Cash discount" field.
If the shortfall is not a cash discount amount, the invoice will continue to be set to "partially paid" and will be transferred to the dunning process after the payment deadline has expired. You can either dun the shortfall there or post it as a cash discount via the icon
You can find more information in our manual: