### 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
if (_signals.has(p_signal)) {
		return true;
	}
	if (base.is_valid()) {
		return base->has_script_signal(p_signal);
	}
#ifdef TOOLS_ENABLED
	else if (base_cache.is_valid()) {
		return base_cache->has_script_signal(p_signal);
	}
#endif
	return false;
}
void GDScript::_get_script_signal_list(List<MethodInfo> *r_list, bool p_include_base) const {
	for (const KeyValue<StringName, MethodInfo> &E : _signals) {
		r_list->push_back(E.value);
	}
	if (!p_include_base) {
		return;
	}
	if (base.is_valid()) {
		base->get_script_signal_list(r_list);
	}
#ifdef TOOLS_ENABLED
	else if (base_cache.is_valid()) {
		base_cache->get_script_signal_list(r_list);
	}
#endif
}
void GDScript::get_script_signal_list(List<MethodInfo> *r_signals) const {