Initially a Purchase Order with a quantity of 1.000 is created by the supply chain department. A prepayment of 50% is required, and has been posted and paid. The Purchase Order has been released. Now a quantity of 1.050 is received. The company allows this and has created an Over-Receipt Code to handle this, which allows the warehouse to put in a quantity to receive of 1.050. So far all good...
But posting the receipt an error occur that the prepayment has to be adjusted because of the extra quantity of 50. The warehouse has to ask the supply chain department to correct the prepayment percentage to fit the original amount, or to put the extra quantity of 50 on a separate line with no prepayment required.
As a receipt are later in the process than prepayment, receipt by using an Over-Receipt Code should in my opinion not be included in the calculation of prepayment.