On orders, you are able to close line-items manually when you do not intend to fulfill open items on the order.
For example, you sell ten widgets to a customer and have already fulfilled five of them. Then, you discontinue the item and cannot fulfill the remaining five. If you close the line manually instead of changing the quantity, you retain a record of how many were ordered originally.
To close a line item on an order manually:
Go to Transactions > Sales > Enter Sales Orders > List.
Click Edit next to the order with the line you want to close.
On the Items subtab of the order, click the line you want to close.
Check the box in the Closed column, and click Done.
If you are going to close a line item on a sales order manually, you must bill the sales order BEFORE you close the line. When all lines on a sales order are fulfilled or closed manually, the sales order will be removed from the billing queue and the receiving queue.