How to change the templates update-safe

Hi,
I’ve just updated a site from version 8 to version 10. It was a nightmare. We all know: it’s a terrible idea to put template files in a plugin folder. However, I know that this was necessary due to the crazy Envato conditions. Having said this, is it now possible to apply the mods update-safe? And why are files still in the theme folder that are now loaded from the plugin folder? For example: /parts/header/header-menu.php.

Thanks, Mike

Sorry, it was an update from 8 to 9. Bad enough. But then I updated to 10. This was even worse. You don’t have to answer this post Please, see my other posts here and here.