Theme updates always overwrite any changes you make to theme files. That's the way updates work.
They should not overwrite changes you make in your theme options, but if there is a way to back up theme options, it doesn't hurt to do that. (Take a screenshot, if nothing else.)
Depending on how much customization you've been doing, you have a couple of different ways to avoid having to repeat your changes every time there is a theme update.
First, as a couple of others have mentioned, is to make a child theme. This is what you will need to do if you have made any changes to the functions.php file or to any page templates. Child themes were invented specifically to avoid the overwrite problem. (Well, and to make it easy to build new themes that were a lot like old ones.)
The second is to use a Custom CSS plugin. If all you are changing is the stylesheet, then you can use something like the Custom CSS feature in Jetpack to make the changes, without having to create a whole child theme. (But save your own copy of that CSS in a text file somewhere, just to be safe.) If you are not using other features from Jetpack, find a different plugin for custom CSS, or just write an additional stylesheet and then summon it in the header. (You will need to replace that link and possibly re-upload the stylesheet after upgrades.)