The email templates are a confusing part of Magento, but hereâs what worked for me, and it doesnât get changed everytime you do an update of the core code (like some solutions):
In Admin > System > transactional emails click âAdd new templateâ
Then under âLoad default templateâ select the default template that you want to base your new template on from the dropdown. (This just saves you writing them from scratch).
Click âLoad Templateâ
Under âTemplate Information, enter a new name (very important to id your new email from the default one!), then edit away to your hearts content changing whatever you want, and deleting the dummy phone and email address.
When you are happy, click âsave templateâ
Repeat for as many as you want changed.
Go to System > Configuration > Sales > sales emails and change the selection by choosing your new email template names from the dropdown.
That should do it. And your emails wonât revert back to the default when you next upgrade Magento.