Since updating to the new Shopify integration version we're running into an issue.
If you click 'Create Another Shipment' in Shipstation, and create a blank shipment, then create a label for just the blank shipment, this marks the entire order in Shopify as Fulfilled.
I would think that since no line items were actually shipped in ShipStation, it would not fulfill the order, and leave it as Unfulfilled in Shopify (or at the most it would show as 'Partially Fulfilled' in Shipstation).
We use this process to ship items in one of our regions to another region for pick up (so the address pre-populates on the shipping label), without prompting the Shopify notifications (which are triggered by the status update).
Right now if we use this process the customer gets a notification that their order is ready for pickup, when the actual items on the order haven't been shipped in ShipStation. We're having to use an external shipping service, which causes delays in our workflows.