### 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
RBSet<GDScript *> dependencies;
	_get_dependencies(dependencies, this);
	dependencies.erase(this);
	return dependencies;
}
RBSet<GDScript *> GDScript::get_inverted_dependencies() {
	RBSet<GDScript *> inverted_dependencies;
	List<GDScript *> scripts;
	{
		MutexLock lock(GDScriptLanguage::singleton->mutex);
		SelfList<GDScript> *elem = GDScriptLanguage::singleton->script_list.first();
		while (elem) {
			scripts.push_back(elem->self());
			elem = elem->next();
		}
	}
	for (GDScript *scr : scripts) {
		if (scr == nullptr || scr == this || scr->destructing) {
			continue;
		}
		RBSet<GDScript *> scr_dependencies = scr->get_dependencies();
		if (scr_dependencies.has(this)) {
			inverted_dependencies.insert(scr);
		}
	}
	return inverted_dependencies;
}
RBSet<GDScript *> GDScript::get_must_clear_dependencies() {