### 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
subclass.id = E.value->get_instance_id();
		subclass.fully_qualified_name = E.value->fully_qualified_name;
		weak_subclasses.push_back(subclass);
	}
	
	for (KeyValue<StringName, Ref<GDScript>> &E : subclasses) {
		p_clear_data->scripts.insert(E.value);
	}
	subclasses.clear();
	
	for (KeyValue<StringName, Variant> &E : constants) {
		GDScript *gdscr = _get_gdscript_from_variant(E.value);
		if (gdscr != nullptr) {
			p_clear_data->scripts.insert(gdscr);
		}
	}
	constants.clear();
	
	for (int i = 0; i < weak_subclasses.size(); i++) {
		ClassRefWithName subclass = weak_subclasses[i];
		Object *obj = ObjectDB::get_instance(subclass.id);
		if (!obj) {
			continue;
		}
		
		GDScriptLanguage::get_singleton()->add_orphan_subclass(subclass.fully_qualified_name, subclass.id);
	}
}
#ifdef DEBUG_ENABLED
String GDScript::debug_get_script_name(const Ref<Script> &p_script) {