Here is a handy plugin that lets you split your orders into separate orders based on category, product availability, and other factors. Split Order for WooCommerce Plugin lets you split orders per category, so you can process items individually. You can also use this to split carts that have in-stock and backordered products in them.
The Split Order extension provides different order IDs for split orders. It works with the WooCommerce Multi Locations Inventory Management plugin, so you can handle orders from different locations. Admins have the option to split orders manually. TechSpwan is the developer behind this plugin.