### 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
Variant value = p_notification;
	const Variant *args[1] = { &value };
	List<GDScript *> pl;
	GDScript *sptr = script.ptr();
	while (sptr) {
		if (p_reversed) {
			pl.push_back(sptr);
		} else {
			pl.push_front(sptr);
		}
		sptr = sptr->_base;
	}
	for (GDScript *sc : pl) {
		HashMap<StringName, GDScriptFunction *>::Iterator E = sc->member_functions.find(GDScriptLanguage::get_singleton()->strings._notification);
		if (E) {
			Callable::CallError err;
			E->value->call(this, args, 1, err);
			if (err.error != Callable::CallError::CALL_OK) {
				
			}
		}
	}
}
String GDScriptInstance::to_string(bool *r_valid) {