### 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
}
		clear_data->clear();
	}
}
GDScript::~GDScript() {
	if (destructing) {
		return;
	}
	destructing = true;
	clear();
	{
		MutexLock lock(GDScriptLanguage::get_singleton()->mutex);
		while (SelfList<GDScriptFunctionState> *E = pending_func_states.first()) {
			
			
			pending_func_states.remove(E);
			GDScriptFunctionState *state = E->self();
			ObjectID state_id = state->get_instance_id();
			state->_clear_connections();
			if (ObjectDB::get_instance(state_id)) {
				state->_clear_stack();
			}
		}
	}
	{
		MutexLock lock(GDScriptLanguage::get_singleton()->mutex);
		script_list.remove_from_list();
	}
}
bool GDScriptInstance::set(const StringName &p_name, const Variant &p_value) {