Our 3PL uses Shipstation as their shipping software, which interfaces with our Shopify setup. A few times a month a new label needs to be printed, which is given a different tracking number than the original one sent out to a customer. However, this information is then imported from Ship Station to Shopify as a "note" and nobody is notified.
Has anyone seen this before who might know how to clean up the integration?
Your 3PL probably made a bad decision choosing Shipstation. Shipstation has lots of issues that a better 3PL software won't have. I would recommend you switch. If that is something you'd consider, check out OTW Shipping.