### 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
#ifdef TOOLS_ENABLED
		r_list->push_back(sptr->get_class_category());
#endif 
		for (const PropertyInfo &E : props) {
			r_list->push_back(E);
		}
		if (!p_include_base) {
			break;
		}
		props.clear();
		sptr = sptr->_base;
	}
}
void GDScript::get_script_property_list(List<PropertyInfo> *r_list) const {
	_get_script_property_list(r_list, true);
}
bool GDScript::has_method(const StringName &p_method) const {
	return member_functions.has(p_method);
}
bool GDScript::has_static_method(const StringName &p_method) const {
	return member_functions.has(p_method) && member_functions[p_method]->is_static();
}
MethodInfo GDScript::get_method_info(const StringName &p_method) const {
	HashMap<StringName, GDScriptFunction *>::ConstIterator E = member_functions.find(p_method);
	if (!E) {
		return MethodInfo();
	}
	return E->value->get_method_info();
}
bool GDScript::get_property_default_value(const StringName &p_property, Variant &r_value) const {