Changes made directly to the HTML code inside the Salesforce Email template will not be visible in the Editor. All changes must be made directly through the Editor in order for them to persist and show up in the Editor the next time you edit. You can still make the change directly to the HTML but just be aware that these changes will not be picked up by the Editor and will be overridden the next time you save the template from the Editor. The reason for that is because the app stores the email design in a different file and that file can only be updated through the editor.