I have reproduced the issue on the latest CLI version. Yes, I am on the latest version I have searched existing posts and this report is not a duplicate. Yes, this isn’t a duplicate In which of these areas are you experiencing a problem? Theme Expected behavior Pushes local version of JSON change…

--theme-editor-sync deletes JSON files when modified externally (e.g., by AI coding tools)

Taksh_Shah January 16, 2026, 6:55pm 9

@Josh-Shopify cross-posting this here because I feel it maybe related - maybe something in JSON diffing.

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