X3 has the ability to apply prepayments against sales orders. However, when a partial shipment and invoice is done to the order, the system automatically applies the entire prepayment against the partial shipment. For example, if payment terms says 50% now, and 50% after shipment, and we have received 50% of the order amount as prepayment, when we ship only half of the order, the system will apply the entire prepayment to the partial shipment and saying that the customer does not owe us any additional amount.

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