Edit Processing Order Email

I am trying to add some texts in the processing order email template. I send a processing order email for every purchase made in the funnel process. I was able to edit the email, but the problem is when a user makes initial order, he doesn’t get the edited email but when the user purchases upsell order, he gets the edited email.

I figure out that somehow woocommerce is sending the original/root email template on initial orders, and then It would send the copied/override email on upsell purchases. Any idea how to fix this?

Summary: Customers get different email templates. They get woocommerce root email when they place initial order and then they get an edited email template when they purchase any upsell order.