Dear Rob King,
You custom changes to theme will be lost on theme update, where as your customizer setting and widgets will still remains.
Note: Please do back up of your whole site so you can take a action when you lost some useful setting of your site.. Normally we use duplicator plugin to make a backup.https://wordpress.org/plugins/duplicator/.
Here is the video tutorials how to use duplicator and save it to your local computer https://www.youtube.com/watch?v=VdvOGV2eIjE.
Thanks