Godot claims broken dependencies, files are still where they're supposed to be, can't fix them

[TheCommandoChicken]

Tested versions

Reproducible in 4.2.stable

System information

Godot v4.2.1.stable - Windows 10.0.19045 - Vulkan (Forward+) - integrated AMD Radeon(TM) Graphics (Advanced Micro Devices, Inc.; 31.0.12029.10015) - AMD Athlon Silver 3050U with Radeon Graphics (2 Threads)

Issue description

As a result of a Git desync, my Godot editor refuses to load the default scene, claiming broken dependencies. No files outside of the .godot folder are missing or changed, as that was the folder that got desynced, and clicking on "Fix Dependencies" shows every file in the correct location, with no option to apply the fixes. Deleting the .godot folder does not fix the issue.

Steps to reproduce

These are the steps I followed that resulted in the desync

• Add /.godot to gitignore
• Delete .godot folder from repository and commit changes
• Pull repository on local device

Minimal reproduction project (MRP)

Attached is a stripped down version of the project I was working on. MRP.zip

[github-actions[bot]]

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[nalmeth]

Can confirm this problem. In 4.3. I have a scene that claims missing dependency, but the file is there. Unable to fix it. Cannot open scene with "open anyway", get "Error while parsing..." message. This is a huge problem. This has made my project completely broken.