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The theme updater at app.ecomelixir.com preserves your settings and section configurations. For the basic procedure see Updating. This guide covers the part that matters when a store is live: updating without risking the storefront, and getting back if something goes wrong.
Never run an update directly on your published theme. Duplicate it, update the duplicate, test it, and publish only after it passes.

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The safe update sequence

1

Duplicate the live theme

In Shopify admin, Online Store → Themes → ⋯ → Duplicate. You now have a copy to work on and an untouched original.
2

Download a backup

⋯ → Download theme file on the original. Keep the ZIP somewhere you can find it.
3

Record your versions

Note the version you are on and the version you are moving to. You will need both if you have to ask for help.
4

List your custom code and critical apps

Write down every custom Liquid, CSS, or JavaScript change, and the apps your store cannot trade without.
5

Update the duplicate

Run the updater against the duplicate, never the published theme.
6

Test the duplicate

Work through the checklist below before publishing anything.
7

Publish

Publish the updated copy, then recheck the live store. Keep the previous theme in the library until the new one has been stable for a few days.

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Post-update test checklist

Test in an incognito window as well as the editor preview. The theme editor can show a different result from the live storefront.

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What is preserved and what is not

Custom CSS you entered in Theme settings → Custom CSS survives an update, because it lives in settings rather than in code. The selectors inside it can still go stale if class names changed. See Custom CSS.

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Stable or beta

Do not install a beta on a live store without a backup and a tested rollback. Beta releases can change between builds.

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Recovering from a bad update

Do not publish the updated copy. Your original theme is still in the Theme Library, untouched, because you updated a duplicate. Go back to it. Then compare the two copies to identify what is missing and raise a ticket with that list.
Check the sections that changed for their own color and style overrides. An update can reset a section that was relying on a default which has since moved. See Set up your brand for how palette inheritance works.
Class names can change between versions. Re-inspect the element, get the current class name, and update the selector. See Custom CSS.
Confirm the dashboard still shows your store as connected, and that the license is assigned to this store. See Activate your license.If it still will not run, move to the new version by hand instead, see Updating manually when the merger fails.
Republish the previous theme from the Theme Library immediately to restore trading, then investigate on the duplicate. If the previous theme is gone, upload the backup ZIP you downloaded.

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If it is still not resolved

  • Your current and target theme versions
  • A list of the missing sections or files
  • Screenshots of before and after
  • Your custom code locations and your app list