### 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
}
		ERR_FAIL_V_MSG(nullptr, "Error constructing a GDScriptInstance.");
	}
	if (p_argcount < 0) {
		return instance;
	}
	initializer = _super_constructor(this);
	if (initializer != nullptr) {
		initializer->call(instance, p_args, p_argcount, r_error);
		if (r_error.error != Callable::CallError::CALL_OK) {
			instance->script = Ref<GDScript>();
			instance->owner->set_script_instance(nullptr);
			{
				MutexLock lock(GDScriptLanguage::singleton->mutex);
				instances.erase(p_owner);
			}
			ERR_FAIL_V_MSG(nullptr, "Error constructing a GDScriptInstance.");
		}
	}
	
	return instance;
}
Variant GDScript::_new(const Variant **p_args, int p_argcount, Callable::CallError &r_error) {
	
	if (!valid) {
		r_error.error = Callable::CallError::CALL_ERROR_INVALID_METHOD;
		return Variant();
	}
	r_error.error = Callable::CallError::CALL_OK;
	Ref<RefCounted> ref;