[Bug]: theme pull sometimes empties existing files

[verdant-spark]

Please confirm that you have:

• Searched existing issues to see if your issue is a duplicate. (If you’ve found a duplicate issue, feel free to add additional information in a comment on it.)
• Reproduced the issue in the latest CLI version.

In which of these areas are you experiencing a problem?

Theme

Expected behavior

Theme pull should only pull changed files from remote

Actual behavior

Occasionally, theme pull pulls existing files as an empty string; these need to be caught and disregarded. There doesn't seem to be any rhyme or reason to which files are pulled as empty: it's inconsistent in both frequency and the files which are pulled as empty. It's impossible to replicate in any meaningful way, but it's happened in more than one store over the last few days.

Verbose output

No error actually logged - just the change indicating that a file is now empty.

Reproduction steps

Operating System

Windows 11

Shopify CLI version (shopify --version)

@shopify/cli/3.76.2 win32-x64 node-v22.13.0

Shell

cmd.exe

Node version (run node -v if you're not sure)

v22.13.0

What language and version are you using in your application?

No response