You know, I wonder if someone who has orders.php inabled to work with edit orders, not hidden as is an option with super orders, could do a test to see if the email coming from edit_orders.php when you update from there is the email_template_default.
I am working with 1.3.9h Edit Orders WITHOUT Super Orders. When the same product was updated from orders.php and edit_order.php, respectively, it generated two emails which are clearly different...not by much, but just different. The problem for me is I have no idea how to find the template used for each respective email.

HTH.

JJ