### 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
}
	}
	for (KeyValue<Ref<GDScript>, HashMap<ObjectID, List<Pair<StringName, Variant>>>> &E : to_reload) {
		Ref<GDScript> scr = E.key;
		scr->reload(p_soft_reload);
		
		for (KeyValue<ObjectID, List<Pair<StringName, Variant>>> &F : E.value) {
			List<Pair<StringName, Variant>> &saved_state = F.value;
			Object *obj = ObjectDB::get_instance(F.key);
			if (!obj) {
				continue;
			}
			if (!p_soft_reload) {
				
				obj->set_script(Variant());
			}
			obj->set_script(scr);
			ScriptInstance *script_inst = obj->get_script_instance();
			if (!script_inst) {
				
				if (!scr->pending_reload_state.has(obj->get_instance_id())) {
					scr->pending_reload_state[obj->get_instance_id()] = saved_state;
				}
				continue;
			}
			if (script_inst->is_placeholder() && scr->is_placeholder_fallback_enabled()) {
				PlaceHolderScriptInstance *placeholder = static_cast<PlaceHolderScriptInstance *>(script_inst);
				for (List<Pair<StringName, Variant>>::Element *G = saved_state.front(); G; G = G->next()) {
					placeholder->property_set_fallback(G->get().first, G->get().second);
				}