I think I can solve your problem with Order Automator. It's an app to automate order processing tasks. I led the development on it, and we often do custom features for stores if the app's current feature set doesn't solve the problem.
If that's appealing to you, send a contact from the app page with the details of exactly what you'd like automated, and someone from my team will help you solve your problem.
No we have not found a suitable APP to do this. We are still relying on tags, adding notes to orders and using an EXPORT to keep track of each line item. It is very tedious and a shame that a company of shopify's status dropped the ball on such an integral part of order fulfilment, especially at times like these when goods and services are taking longer to produce/ship.