Orders will not be marked as old unless you view them using the View functions in the Orders section of the Yahoo! Store Manager. You should be able to view a single new order or a range of new orders using the View feature.
If you click on the links to your orders in the list generated by the Summarize function in the Orders section, those orders will not be marked as old and will continue to appear as new orders. Also, if you reference new orders through any other links on the Store Manager page, such as from the Repeats or Track Links page, then the orders would still not be considered "viewed" and would not be marked as old.