### 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_vararg_method(METHOD_FLAGS_DEFAULT, "new", &GDScript::_new, MethodInfo("new"));
}
void GDScript::set_path(const String &p_path, bool p_take_over) {
	if (is_root_script()) {
		Script::set_path(p_path, p_take_over);
	}
	String old_path = path;
	path = p_path;
	path_valid = true;
	GDScriptCache::move_script(old_path, p_path);
	for (KeyValue<StringName, Ref<GDScript>> &kv : subclasses) {
		kv.value->set_path(p_path, p_take_over);
	}
}
String GDScript::get_script_path() const {