### 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
}
				if (updatable->transferred) {
					func_ptrs_to_update_main_thread.mutex.unlock();
				}
			}
			if (destroy) {
				DEV_ASSERT(updatable != &func_ptrs_to_update_main_thread);
				memdelete(updatable);
			}
		}
	}
	RBSet<GDScript *> must_clear_dependencies = get_must_clear_dependencies();
	for (GDScript *E : must_clear_dependencies) {
		clear_data->scripts.insert(E);
		E->clear(clear_data);
	}
	for (const KeyValue<StringName, GDScriptFunction *> &E : member_functions) {
		clear_data->functions.insert(E.value);
	}
	member_functions.clear();
	for (KeyValue<StringName, MemberInfo> &E : member_indices) {
		clear_data->scripts.insert(E.value.data_type.script_type_ref);
		E.value.data_type.script_type_ref = Ref<Script>();
	}
	for (KeyValue<StringName, MemberInfo> &E : static_variables_indices) {
		clear_data->scripts.insert(E.value.data_type.script_type_ref);
		E.value.data_type.script_type_ref = Ref<Script>();
	}
	static_variables.clear();
	static_variables_indices.clear();