### 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
return true;
			}
		}
		top = top->_base;
	}
	return false;
}
void GDScript::_get_property_list(List<PropertyInfo> *p_properties) const {
	p_properties->push_back(PropertyInfo(Variant::STRING, "script/source", PROPERTY_HINT_NONE, "", PROPERTY_USAGE_NO_EDITOR | PROPERTY_USAGE_INTERNAL));
	List<const GDScript *> classes;
	const GDScript *top = this;
	while (top) {
		classes.push_back(top);
		top = top->_base;
	}
	for (const List<const GDScript *>::Element *E = classes.back(); E; E = E->prev()) {
		Vector<_GDScriptMemberSort> msort;
		for (const KeyValue<StringName, MemberInfo> &F : E->get()->static_variables_indices) {
			_GDScriptMemberSort ms;
			ms.index = F.value.index;
			ms.name = F.key;
			msort.push_back(ms);
		}
		msort.sort();
		for (int i = 0; i < msort.size(); i++) {
			p_properties->push_back(E->get()->static_variables_indices[msort[i].name].property_info);
		}
	}
}
void GDScript::_bind_methods() {