### 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
_get_script_signal_list(r_signals, true);
}
GDScript *GDScript::_get_gdscript_from_variant(const Variant &p_variant) {
	Object *obj = p_variant;
	if (obj == nullptr || obj->get_instance_id().is_null()) {
		return nullptr;
	}
	return Object::cast_to<GDScript>(obj);
}
void GDScript::_get_dependencies(RBSet<GDScript *> &p_dependencies, const GDScript *p_except) {
	if (p_dependencies.has(this)) {
		return;
	}
	p_dependencies.insert(this);
	for (const KeyValue<StringName, GDScriptFunction *> &E : member_functions) {
		if (E.value == nullptr) {
			continue;
		}
		for (const Variant &V : E.value->constants) {
			GDScript *scr = _get_gdscript_from_variant(V);
			if (scr != nullptr && scr != p_except) {
				scr->_get_dependencies(p_dependencies, p_except);
			}
		}