### 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
	_update_exports_down(false);
#endif
}
#ifdef TOOLS_ENABLED
void GDScript::_update_exports_down(bool p_base_exports_changed) {
	bool cyclic_error = false;
	bool changed = _update_exports(&cyclic_error, false, nullptr, p_base_exports_changed);
	if (cyclic_error) {
		return;
	}
	HashSet<ObjectID> copy = inheriters_cache; 
	for (const ObjectID &E : copy) {
		Object *id = ObjectDB::get_instance(E);
		GDScript *s = Object::cast_to<GDScript>(id);
		if (!s) {
			continue;
		}
		s->_update_exports_down(p_base_exports_changed || changed);
	}
}
#endif
String GDScript::_get_debug_path() const {