### 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
ClassDB::bind_method(D_METHOD("new"), &GDScriptNativeClass::_new);
}
Variant GDScriptNativeClass::_new() {
	Object *o = instantiate();
	ERR_FAIL_NULL_V_MSG(o, Variant(), "Class type: '" + String(name) + "' is not instantiable.");
	RefCounted *rc = Object::cast_to<RefCounted>(o);
	if (rc) {
		return Ref<RefCounted>(rc);
	} else {
		return o;
	}
}
Object *GDScriptNativeClass::instantiate() {
	return ClassDB::instantiate(name);
}
Variant GDScriptNativeClass::callp(const StringName &p_method, const Variant **p_args, int p_argcount, Callable::CallError &r_error) {
	if (p_method == SNAME("new")) {
		
		return Object::callp(p_method, p_args, p_argcount, r_error);
	}
	MethodBind *method = ClassDB::get_method(name, p_method);
	if (method && method->is_static()) {
		
		return method->call(nullptr, p_args, p_argcount, r_error);
	}
	r_error.error = Callable::CallError::CALL_ERROR_INVALID_METHOD;
	return Variant();
}
GDScriptFunction *GDScript::_super_constructor(GDScript *p_script) {