When you have completed a pick, click the shipped button, the order on the My account page updates with the message: Your order is shipped. So, from vs 2.4.6 we added the option to split shipments, so now you will be able to e.g. ship item 1 and 2, then when you have the missing product back in stock you can ship again. When shipping the second time (or more) a new message will be updated on the order: Your order is shipped. This is shipment #2 of your order.
Order details
Every order line has (from vs 2.4.6 an option in settings to add) pick status below the product name. This will show the customer that the ordered item is in progress (is picked). This status can be handy for the customer if the order shipment is split into several sendings.
