If you use an app that adds support for pickup/collection identifiers during checkout, it's likely that the app stores the pickup identifier in a custom order note. The app should specify the name of the custom order note field it uses or you will have specified this in the app setup.
Enter the name of the custom order note field into the Pickup Identifier Key field in your Shopify advanced settings, and click Save.
From now on, if the custom order note for pickup identifiers has a value, Shiptheory will download it.

If you encounter any issues, please feel free to contact our support team. You can call us on 0117 403 4313 (UK) / +1 (629) 666-6726 (US) or reach us online here.