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.
I changed to Shopify in the new year, from WIX - as WIX was horrible for ecommerce. However, even WIX allows you to partially fulfill both pick up and shipped orders.
I shouldn't have to pay more money each month for a simple request, it's really disappointing that Shopify hasn't figured this out yet, especially given COVID protocols and shipments being delayed.
I've tried several apps to integrate but all of them are made for more complex fulfillment/dropshipping issues. They should have the same backend solution they do for fulfilling a shipped order as they do for a pick up order.
Please, if anyone comes across a solution - I'm all ears! This is a painfully tedious piece of inventory to manage.