Netsuite - Customer Deposits Auto Applied

In netsuite if there is a customer deposit that is applied to Sales Order and then an order gets billed into an invoice the customer deposit auto applies to the invoice. Invoiced does not recognize customer deposits. Therefore, there could be an invoice that was created with a customer deposit applied against it and has a balance of $0. Invoiced will not recognize the customer deposit and therefore the customer still gets billed. Invoiced and Netsuite therefore are not in sync