### 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
for (const KeyValue<StringName, MemberInfo> &E : static_variables_indices) {
		if (E.value.index == p_idx) {
			return E.key;
		}
	}
	return "<error>";
}
Ref<GDScript> GDScript::get_base() const {
	return base;
}
bool GDScript::inherits_script(const Ref<Script> &p_script) const {
	Ref<GDScript> gd = p_script;
	if (gd.is_null()) {
		return false;
	}
	const GDScript *s = this;
	while (s) {
		if (s == p_script.ptr()) {
			return true;
		}
		s = s->_base;
	}
	return false;
}
GDScript *GDScript::find_class(const String &p_qualified_name) {