### 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
HashMap<ObjectID, List<Pair<StringName, Variant>>> &map = to_reload[scr];
			while (scr->instances.front()) {
				Object *obj = scr->instances.front()->get();
				
				List<Pair<StringName, Variant>> state;
				if (obj->get_script_instance()) {
					obj->get_script_instance()->get_property_state(state);
					map[obj->get_instance_id()] = state;
					obj->set_script(Variant());
				}
			}
#ifdef TOOLS_ENABLED
			while (scr->placeholders.size()) {
				Object *obj = (*scr->placeholders.begin())->get_owner();
				
				if (obj->get_script_instance()) {
					map.insert(obj->get_instance_id(), List<Pair<StringName, Variant>>());
					List<Pair<StringName, Variant>> &state = map[obj->get_instance_id()];
					obj->get_script_instance()->get_property_state(state);
					obj->set_script(Variant());
				} else {
					
					scr->placeholders.erase(*scr->placeholders.begin());
				}
			}
#endif
			for (const KeyValue<ObjectID, List<Pair<StringName, Variant>>> &F : scr->pending_reload_state) {
				map[F.key] = F.value; 
			}