### Godot version

v4.1.beta.custom_build [72b59325c]

### System information

Windows 10, Vulkan

### Issue description

This has been plaguing me for a while in my main project. I can only partially reproduce it in a MRP:
When placing a binary mesh resource imported from a .glb file into a MeshInstance3D, it will be gone upon restart. It doesn't seem to happen to every resource, but I've had MIs that were fine and then start doing it out of nowhere.
I thought it was going to be related to materials due to things like https://github.com/godotengine/godot/issues/77007 but I can reliably trigger it with the steps listed below.
I have done limited testing on .tres files because I usually use .res for size/performance, but in the MRP .tres doesn't seem to trigger it, so perhaps it doesn't affect those.

Note on the Steps to reproduce: you have to delete the test_cube.res and redo the steps to trigger the bug again, but in my main project the affected resources always disappear.

### Steps to reproduce

1. Double click test_cube.glb
2. Click the mesh (test_cube_Cube_097), set save to file path as: res://test_cube.res
3. Make sure to click the little folder icon and then Save (this seems to make it consistent to proc)
4. Press Reimport
5. Drag the test_cube.res to the Mesh slot of the MeshInstance3D
6. Ctrl+s to save
7. Project -> Reload current project
8. Mesh is no longer in the MeshInstance3D

### Minimal reproduction project

[binary res bug.zip](https://github.com/godotengine/godot/files/11681009/binary.res.bug.zip)
String fscache = EditorPaths::get_singleton()->get_project_settings_dir().path_join("filesystem_update4");
	Ref<FileAccess> f = FileAccess::open(fscache, FileAccess::WRITE);
	ERR_FAIL_COND_MSG(f.is_null(), "Cannot create file '" + fscache + "'. Check user write permissions.");
	for (const String &E : late_update_files) {
		f->store_line(E);
	}
}
Vector<String> EditorFileSystem::_get_dependencies(const String &p_path) {
	
	
	
	if (ResourceFormatImporter::get_singleton()->recognize_path(p_path)) {
		const String &internal_path = ResourceFormatImporter::get_singleton()->get_internal_resource_path(p_path);
		if (!internal_path.is_empty() && !FileAccess::exists(internal_path)) { 
			return Vector<String>();
		}
	}
	List<String> deps;
	ResourceLoader::get_dependencies(p_path, &deps);
	Vector<String> ret;
	for (const String &E : deps) {
		ret.push_back(E);
	}
	return ret;
}
String EditorFileSystem::_get_global_script_class(const String &p_type, const String &p_path, String *r_extends, String *r_icon_path) const {