### 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 (int i = 1; result != nullptr && i < class_names.size(); i++) {
		String current_name = class_names[i];
		if (HashMap<StringName, Ref<GDScript>>::Iterator E = result->subclasses.find(current_name)) {
			result = E->value.ptr();
		} else {
			
			return nullptr;
		}
	}
	return result;
}
bool GDScript::has_class(const GDScript *p_script) {
	String fqn = p_script->fully_qualified_name;
	if (fully_qualified_name.is_empty() && fqn.get_slice("::", 0).is_empty()) {
		return p_script == this;
	} else if (fqn.begins_with(fully_qualified_name)) {
		return p_script == find_class(fqn.trim_prefix(fully_qualified_name));
	}
	return false;
}
GDScript *GDScript::get_root_script() {
	GDScript *result = this;
	while (result->_owner) {
		result = result->_owner;
	}
	return result;
}
RBSet<GDScript *> GDScript::get_dependencies() {