My understanding is that when taking a ""Deposit"" on a Sales Order, you could turn on the ""PAY BALANCE"" Field. Then, when the order final invoices it will ""automatically"" charge the balance of the invoice. Are you sure that they did a Deposit on the sales order originally, and not a PreAuth?
But the help files say something slightly different; it says a Pre-Auth is done for the balance... Maybe in this situation the ""Pre-Auth"" expired; and that is what makes this order different than other orders previously?
""Pay Balance
Select this check box to pay the balance of the order using a credit card. If this check box is selected and you click Submit Card, the deposit that is entered will be processed and the remaining order balance will be pre-authorized. The remaining balance will be processed when the Daily Sales Journal is printed. Clear this check box to pay only the deposit using a credit card.
This field is available only for standard orders and backorders, and if Deposit/Sale is selected in the Transaction Type field.