### 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();
	RBSet<GDScript *> must_clear_dependencies;
	HashMap<GDScript *, RBSet<GDScript *>> inverted_dependencies;
	for (GDScript *E : dependencies) {
		inverted_dependencies.insert(E, E->get_inverted_dependencies());
	}
	RBSet<GDScript *> cant_clear;
	for (KeyValue<GDScript *, RBSet<GDScript *>> &E : inverted_dependencies) {
		for (GDScript *F : E.value) {
			if (!dependencies.has(F)) {
				cant_clear.insert(E.key);
				for (GDScript *G : E.key->get_dependencies()) {
					cant_clear.insert(G);
				}
				break;
			}
		}
	}
	for (KeyValue<GDScript *, RBSet<GDScript *>> &E : inverted_dependencies) {
		if (cant_clear.has(E.key) || ScriptServer::is_global_class(E.key->get_fully_qualified_name())) {
			continue;
		}
		must_clear_dependencies.insert(E.key);
	}
	cant_clear.clear();
	dependencies.clear();
	inverted_dependencies.clear();
	return must_clear_dependencies;
}
bool GDScript::has_script_signal(const StringName &p_signal) const {