I'm not too sure about this one, but have you checked out the "Bulk Fulfillment" app in the app store? It might be the solution to your issue here.
Let me know what you think!
AfterShip app can get all the tracking numbers in one place, and allow you to export in CSV.
Tracking numbers imported will be tracked automatically, with the latest tracking results.
Just one thing - AfterShip will only get the tracking numbers added in Shopify in the last 3 days.
Does this work for you?
Exporting orders in csv is directly possible with Shopify. Have you checked our the link : https://help.shopify.com/en/manual/orders/export-orders
The only extra thing that you would need is to segregate the orders based on whether they have been shipped or not. This can be done in the csv file itself.