### 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 extension_list_config_file = GDExtension::get_extension_list_config_file();
	if (extensions.size()) {
		if (extensions_added.size() || extensions_removed.size()) { 
			Ref<FileAccess> f = FileAccess::open(extension_list_config_file, FileAccess::WRITE);
			for (const String &E : extensions) {
				f->store_line(E);
			}
		}
	} else {
		if (loaded_extensions.size() || FileAccess::exists(extension_list_config_file)) { 
			Ref<DirAccess> da = DirAccess::create(DirAccess::ACCESS_RESOURCES);
			da->remove(extension_list_config_file);
		}
	}
	bool needs_restart = false;
	for (int i = 0; i < extensions_added.size(); i++) {
		GDExtensionManager::LoadStatus st = GDExtensionManager::get_singleton()->load_extension(extensions_added[i]);
		if (st == GDExtensionManager::LOAD_STATUS_NEEDS_RESTART) {
			needs_restart = true;
		}
	}
	for (int i = 0; i < extensions_removed.size(); i++) {
		GDExtensionManager::LoadStatus st = GDExtensionManager::get_singleton()->unload_extension(extensions_removed[i]);
		if (st == GDExtensionManager::LOAD_STATUS_NEEDS_RESTART) {
			needs_restart = true;
		}
	}
	return needs_restart;
}
void EditorFileSystem::_bind_methods() {