If you're reading this article, then most probably you're seeing this duplicate emails:
We just want to clarify first that this email is not send by Track123. These are still emails from Shopify, it just shows our logo and name because we are the ones who triggered the emails through our Fulfillment Events setting.
Now, to avoid this, you need to simply turn off Shopify's Out for Delivery and Delivered emails.
By turning this off, only Shipment Update triggers would be sent to Shopify. The orders would still be tagged Delivered/Out for Delivery in Shopify's Order section but only Shipment Update emails would be sent to the customers.
If you want the tracking links on the email be redirected to your tracking page, then please refer to this article: Add your tracking page link to the Shopify email template