There is an option in the WooCommerce settings that shows you how to override and edit the email templates:
WooCommerce -> Settings -> Emails
From there, simply click on the email name or the cog/settings icon to the right of the email template that you would like to modify and you will be presented with the following screen:
Highlighted in Red, is the section that refers to the emails HTML template.
You can click on the 'Copy file to theme' button and this will copy the email template file from:
to your currently active themes folder as a template override:
Update: This was caused by a plugin and was found when I asked OP to disable plugins to test in comments below