Unfortunately, the Amazon API cannot detect if some of the items within an order have been shipped. Once a shipment for the order has been processed, regardless of whether all of the orders products have been shipped, Amazon will update the order within your store as Shipped.
How to use Amazon with ShippingEasy
Why don't my Amazon orders show as Shipped, even when they have?
How do I comply with Amazon's policy for post-dated labels?
How do I process returns for Amazon shipments?
Why is the weight incorrect in ShippingEasy for my Amazon products?