Hey @Bad_Workwear we help retailers in this type of situation all the time. You can check out SKUSavvy which is a full Shopify-based warehouse management system that leverages a visual warehouse layout to organize bin locations within the warehouse.
In the case of retail, each store would be a warehouse that can accept or create transfers from a central warehouse to stores, as well as being able to partially fulfill (or transfer) orders across store locations.
Inventory is automatically updated back to Shopify and SKUSavvy is designed to replace the entirety of Shopify inventory management in a single platform.