Contents of `c_cpp_properties.json` file can get irrecoverably deleted

Environment

• OS and Version: Debian 6.1.0-32-amd64
• VS Code Version: 1.98.2
• C/C++ Extension Version: 1.24.5
• If using SSH remote, specify OS of remote machine: N/A

Bug Summary and Steps to Reproduce

Bug Summary:
After stashing and restoring .vscode/c_cpp_properties.json through git, cpptools will re-populate it's contents with default value deleting old contents.
Also works when temporarily moving or renaming .vscode directory.

Steps to reproduce:

1. Create empty project and initialize git.

   mkdir -p foo/.vscode
   cd foo
   touch main.c
   git init
   git add main.c
   git commit -m 'Initial commit'
   

2. Populate c_cpp_properties.json. Just something that differs from the default.

   echo '{"configurations":[{"name":"Foo"}],"version":4}' > .vscode/c_cpp_properties.json
   

3. Open project folder in vscode and edit main.c. You should see C/C++ configuration is "Foo".
4. Without closing vscode, stash untracked files and then restore them.

   git stash -k -u
   git stash pop
   

5. Switch back to main.c. You should see C/C++ configuration has changed to default ("Linux" in my case).
6. Click C/C++: Edit Configurations (JSON) through bottom right corner or command palette. This action destroys contents of c_cpp_properties.json. If you'd instead close and re-open vscode, you'd be safe.

Configuration and Logs

{"configurations":[{"name":"Foo"}],"version":4}

[C++.log](https://github.com/user-attachments/files/19702057/C%2B%2B.log)
[C++ Diagnostics.log](https://github.com/user-attachments/files/19702056/C%2B%2B.Diagnostics.log)

Other Extensions

• Vim

Additional context

No response

Reproduce the issue with .vscode/c_cpp_properties.json using the listed git stash -k -u and git stash pop steps, then use C/C++: Edit Configurations (JSON) to confirm the overwrite. Read the linked C++ logs while tracing the extension behavior around the restored configuration. Done means the custom Foo configuration remains intact after restoration and editing the JSON configuration.