### 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)
ERR_FAIL_COND_V_MSG(!importing, ERR_INVALID_PARAMETER, "Can only append files to import during a current reimport process.");
	return _reimport_file(p_file, p_custom_options, p_custom_importer, &p_generator_parameters);
}
Error EditorFileSystem::_resource_import(const String &p_path) {
	Vector<String> files;
	files.push_back(p_path);
	singleton->update_file(p_path);
	singleton->reimport_files(files);
	return OK;
}
bool EditorFileSystem::_should_skip_directory(const String &p_path) {
	String project_data_path = ProjectSettings::get_singleton()->get_project_data_path();
	if (p_path == project_data_path || p_path.begins_with(project_data_path + "/")) {
		return true;
	}
	if (FileAccess::exists(p_path.path_join("project.godot"))) {
		
		if (EditorFileSystem::get_singleton()->first_scan) {
			WARN_PRINT_ONCE(vformat("Detected another project.godot at %s. The folder will be ignored.", p_path));
		}
		return true;
	}
	if (FileAccess::exists(p_path.path_join(".gdignore"))) {
		
		return true;
	}
	return false;
}
bool EditorFileSystem::is_group_file(const String &p_path) const {