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I need to dive into this more to see what is actually happening to see if I can fix it. But, I have some sorter term options for you.
First, IF you are customizing by adjusting the theme, please make sure you are using a child theme, NOT the parent theme, or that will reset with every update.
If you’re just talking about your settings in the customizr, what you’re describing should not be happening. While I try to investigate, one thing you can do is use a plugin to backup your settings, that way you can just import them back in if you have a problem like this in the future. Here’s one option: Customizer Export / Import
Yes, is the settingsnon customizer