I would like to change some files in marketplace plugin offline/mall/views/mail/_partials. Any update would make that change undone. But I can add new files to the folder. If the plugin would update to a newer version, would that delete my added files? Or does the update only take effect on the original plugin files?
The update would delete those files. There is pretty much always a way to dynamically extend the code to use your own templates without running the risk of losing your changes though, so if you ask a more specific question in the October Discord server we should be able to help you figure out how to do that.