### Godot version

v4.2.rc.mono.custom_build [ad72de508]

### System information

Windows 10

### Issue description

As I pointed out several times earlier in [#80284](https://github.com/godotengine/godot/pull/80284#issuecomment-1722120503), the references to singletons in `GDScript` are still not updated after the `GDExtension` reload.

https://github.com/godotengine/godot/assets/7782218/f90052a5-0de2-4310-8235-f0b9e2f74b3a

Singletons themselves are updated and work correctly, but references to these singletons are not updated in `@tool` scripts. That is, `Engine.get_singleton` returns the actual working reference, but using the singleton directly through its name causes errors.

### Steps to reproduce

* Clone `4.2.reload_singleton` branch from the MRP repository https://github.com/DmitriySalnikov/gde_test_cases/tree/4.2.reload_singleton
* Build as usual
* Open the project from the `project/` folder
* Add one character to the source code and rebuild
* Focus on the editor to reload extension
* Watch for error spam when calling by singleton name

### Minimal reproduction project

https://github.com/DmitriySalnikov/gde_test_cases/tree/4.2.reload_singleton
script_list(this) {
	{
		MutexLock lock(GDScriptLanguage::get_singleton()->mutex);
		GDScriptLanguage::get_singleton()->script_list.add(&script_list);
	}
	path = vformat("gdscript://%d.gd", get_instance_id());
}
void GDScript::_save_orphaned_subclasses(ClearData *p_clear_data) {
	struct ClassRefWithName {
		ObjectID id;
		String fully_qualified_name;
	};
	Vector<ClassRefWithName> weak_subclasses;
	
	for (KeyValue<StringName, Ref<GDScript>> &E : subclasses) {
		E.value->_owner = nullptr; 
		ClassRefWithName subclass;