### 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
GLOBAL_DEF("debug/gdscript/warnings/enable", true);
	GLOBAL_DEF("debug/gdscript/warnings/exclude_addons", true);
	for (int i = 0; i < (int)GDScriptWarning::WARNING_MAX; i++) {
		GDScriptWarning::Code code = (GDScriptWarning::Code)i;
		Variant default_enabled = GDScriptWarning::get_default_value(code);
		String path = GDScriptWarning::get_settings_path_from_code(code);
		GLOBAL_DEF(GDScriptWarning::get_property_info(code), default_enabled);
	}
#endif 
}
GDScriptLanguage::~GDScriptLanguage() {
	singleton = nullptr;
}
void GDScriptLanguage::add_orphan_subclass(const String &p_qualified_name, const ObjectID &p_subclass) {
	orphan_subclasses[p_qualified_name] = p_subclass;
}
Ref<GDScript> GDScriptLanguage::get_orphan_subclass(const String &p_qualified_name) {
	HashMap<String, ObjectID>::Iterator orphan_subclass_element = orphan_subclasses.find(p_qualified_name);
	if (!orphan_subclass_element) {
		return Ref<GDScript>();
	}
	ObjectID orphan_subclass = orphan_subclass_element->value;
	Object *obj = ObjectDB::get_instance(orphan_subclass);
	orphan_subclasses.remove(orphan_subclass_element);
	if (!obj) {
		return Ref<GDScript>();
	}
	return Ref<GDScript>(Object::cast_to<GDScript>(obj));
}
Ref<GDScript> GDScriptLanguage::get_script_by_fully_qualified_name(const String &p_name) {