Hi @mitchjs 
Without knowing what and how your custom app is meant to “import” data (this could be using a direct REST/GraphQL Admin API request or one of the order-related webhooks), it’s unclear what could be causing this issue. Generally, the shipping line source of an order is the provider of the quoted shipping rate. Keep in mind that our Admin API is versioned quarterly, and changes are announced a year in advance in case migrations are required.
I’d recommend working with a developer who can review the app’s source code and identify the culprit. You can share the below reference docs with the developer as a good place to start as well:
Hope that helps!