### 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
Ref<GDScript> sqscr = p_resource;
	ERR_FAIL_COND_V(sqscr.is_null(), ERR_INVALID_PARAMETER);
	String source = sqscr->get_source_code();
	{
		Error err;
		Ref<FileAccess> file = FileAccess::open(p_path, FileAccess::WRITE, &err);
		ERR_FAIL_COND_V_MSG(err, err, "Cannot save GDScript file '" + p_path + "'.");
		file->store_string(source);
		if (file->get_error() != OK && file->get_error() != ERR_FILE_EOF) {
			return ERR_CANT_CREATE;
		}
	}
	if (ScriptServer::is_reload_scripts_on_save_enabled()) {
		GDScriptLanguage::get_singleton()->reload_tool_script(p_resource, true);
	}
	return OK;
}
void ResourceFormatSaverGDScript::get_recognized_extensions(const Ref<Resource> &p_resource, List<String> *p_extensions) const {
	if (Object::cast_to<GDScript>(*p_resource)) {
		p_extensions->push_back("gd");
	}
}
bool ResourceFormatSaverGDScript::recognize(const Ref<Resource> &p_resource) const {
	return Object::cast_to<GDScript>(*p_resource) != nullptr;
}