How to customize the template of WooCommerce email (even for Multi Vendor but not only)
1. Go in WooCommerce > Settings > Emails and check for the email that you want to edit:
2. After this copy the email template in your theme:
3. Go in your theme folder and search the email template, open and edit it:
In this way the plugin use the theme template and not the original plugin file and you can update your plugin without problem. Of course remember to make a backup copy of this file and restore it after theme update. It's more easy to restore a file instead of open the file and edit it every time you update the plugin.
Another solution are use the child theme (you can follow the previous steps for child theme, too) in this way you can update theme and plugin without any problems. For more information about child theme, please read this post: https://codex.wordpress.org/Child_Themes