How Shopify handles this
Shopify doesn't update an uploaded theme in place. A new version arrives as a new theme in your theme library, next to the one that's live. Your changes in the theme editor (colours, sections, page layouts and your licence key) are saved inside your current theme, so the job is to bring them across.
The good news: your live store keeps running the whole time, and you can switch back with one click.
1. Back up your current theme
In Online Store → Themes, open the menu on your live theme and choose Duplicate. Also choose Download theme file. Shopify emails you a ZIP of the theme with all your settings. Keep it safe.
2. Read the changelog
Check the Changelog on the theme page so you know what changed. If a release notes something specific to do when updating, it will say so there.
3. Choose how to bring your changes across
Option A: set it up again in the editor (simplest, safest). Upload the new ZIP (Add theme → Upload zip file), open Customize, and redo your settings, using your live theme in another tab as a guide. Remember to paste your licence key in Theme settings → License. This is the best choice if you've changed only a few things.
Option B: copy your settings files into the new version (faster for big setups). Your editor changes live in a few JSON files:
config/settings_data.json: theme settings, including colours, fonts and your licence key,templates/*.json: the sections and blocks on each page type,sections/header-group.jsonandsections/footer-group.json: your header and footer.
Unzip the theme file Shopify emailed you and the new version from your Orbital account. Copy those files from your backup into the new version's folders, zip the new version again (the folders like assets and config must sit at the top of the ZIP, not inside another folder), and upload it.
4. Check before you publish
Open the new theme in the editor and preview it. Click through the home page, a collection, a product, the cart and anything you customised. If a release added new sections or settings, they'll be there for you to switch on.