No, you won’t lose your upload and settings when you update the theme. It’ll stay there. But, if you already have edited some files on the theme, of course, you will lose them. As this will overwrite your previous version of the theme’s files. So, you might as well backup your existing theme and re-apply again your edits once you’ve updated the theme. Also, it might be a good way to use Child Themes to prevent losing your code changes.