An individual line item in a claimed shipping order that can't be shipped (for example, customers in the store have purchased all available stock) can be marked as zero inventory. When a line item is market as zero inventory, Order Management sets the inventory of that item for the current site to 0. This prevents further shipping orders that include that item from being allocated to the store until the inventory is updated.
To do this, you must claim the shipping order, and then mark the line items as zero inventory. The shipping order can still be rejected from the Waiting Fulfillment queue after it's initially claimed, or it can be partially shipped.