One of the primary reasons for an order from Shopify showing as "Not Found" in Shiptheory is that it has been archived in Shopify before or at the same time as it is marked as fulfilled.
The order will still come into Shiptheory but will display like below:
The suggested workflow is to archive an order after an order is fulfilled and booked in Shiptheory. Orders that have already been affected by this should be unarchived in Shopify and then retried in Shiptheory.
To do this, first, access the order in Shopify, click "More Actions" and then click "Unarchive":
After this, access the order in your Shiptheory dashboard and hit "retry":
The order should then be complete or ready to book in. If you have any problems with this, please contact support.