Adjusting Invoice amount on wholesale orders

[Storacell]

We are using a wholesale app but not able to remove 2% discounts or other deductions when invoices are paid. For example, when customer’s pay early or have other deductions I am unable to change the invoice amount to receive the amount they actually paid. Does this mean that the orders need to remain in draft mode until it is paid in order to make changes? My issue then is that the product inventory does not come out in draft mode.