Once an order is sent to you, you have the ability to mark individual items out of stock within the order.
Find the order you would like to edit and click anywhere within the Order to be taken to the order details page.
Under the Items Tab, click on Out Of Stock and that item will appear as out of stock to the retailer when they view the order.
If items are back in stock while the order is still in Pending status, you can go back and mark that item as back in stock by clicking on In Stock.
Please note that this action is ONLY marking products out of stock. The order will remain in Pending status until the Accept or Reject button is clicked.