We are seeing the same on a production store, and it goes beyond newly added files.
Setup: live theme connected to a GitHub branch via the GitHub integration. The theme receives changes through the theme editor, Shopify CLI (shopify theme push --only ... --allow-live) and the Admin API (asset uploads). The integration keeps committing (“Update from Shopify for theme …”), the latest commit is from yesterday, so the connection itself is alive.
We compared a fresh full shopify theme pull of the live theme (770 files) with the connected branch at its latest commit:
- ~50 files exist only in the theme, not in the branch: all of them were added via CLI push or Admin API (e.g. a new section and about 50 SVG assets). Same pattern as reported above.
- ~35 files differ in content. Some examples:
- one section file is 0 bytes in the branch but 2.6 KB in the theme
- one snippet was last committed in February, a later fix pushed via CLI never arrived
- several locales/*.schema.json, a CSS asset and customer templates are out of date
- Nothing in the theme admin indicates that the branch is incomplete.
The practical risk: the branch cannot be used as a backup, and “Reset to last commit” would roll the live theme back to an incomplete state (empty section, missing assets). We now treat a full CLI pull as the only reliable backup.
Questions:
- Is this the same root cause as the issue in this thread, or a separate one (existing files not updated / committed empty)?
- Is there a way to force a full re-sync from theme to branch without disconnecting?
- Is there an ETA or a recommended workaround?
Happy to share request IDs from the next CLI push if that helps the investigation.
[this seems the same issue: GitHub integration ignores new files added via `shopify theme push` - #5 by Wes-Dev-Shopify]