ShipStation added the "Use Fulfillable Quantity" setting for connected Shopify stores several months ago. This setting will update the quantity of the items in an order that has been edited in Shopify upon refresh in ShipStation. This setting is still relatively new and has a few limitations. Review the Updating Modified Shopify Orders section of our Shopify help article for more information.
If you'd like this setting to be enabled on your ShipStation account, you must contact our support team and request it.
We'll keep this post in the Started status as our development team addresses some of the limitations present in the current iteration of this feature.
I made a post some time ago here: https://community.shipstation.com/t5/Stores-Carriers-and-Other/Editing-and-removing-line-items-in-Sh...
This post shows how Shipstation can use GraphQL to accurately adjust the order on Shipstation's side to reflect that of Shopifys.
+1 on this request.