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…

Yeah have similar things happen enough times that I just avoid the flag :grimacing: which isn’t a great thing to suggest and the proper thing to do is making an issue here - but it just seems really temperamental. Love the idea of how it’s supposed to work and when it works - it’s AWESOME. But I ha…

Experienced the same, fortunately the file is still there in my IDE and I can just hit Cmd+S to re-save and I have it back

Yes, except occasionally when close the tab in IDE and now it’s just lost in the void.

Thank you for the report! We will look into it.

I was able to recreate this today withbthe verbose flag. I shared the logs with a Shopify Team member where I could reach them directly, as I didn’t want to post something potentially sensitive publicly on here. I do have these steps about how I recreated the issue. I tried to pull changes using t…

I appreciate the follow up info! So we have two different things going on. One is that while running theme dev we have files sometimes deleting, and then we have the scenario where theme dev is running and we call theme pull. I will be working on fixes for both scenarios.

Sorry for the delayed response @Josh-Shopify Just sent you an email with the file. Happy to help if you have more questions for me

@Josh-Shopify cross-posting this here because I feel it maybe related - maybe something in JSON diffing. [image] Theme editor showing false "override changes" prompt Online Store and Theme Development Hi @Taksh_Shah , thanks for reaching out to report this issue…

Hmm. I have not seen that warning before. Will bring it to the team.

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

Shopify CLI and Libraries

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

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