### 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
#ifdef TOOLS_ENABLED
	HashMap<StringName, Variant>::ConstIterator E = member_default_values_cache.find(p_property);
	if (E) {
		r_value = E->value;
		return true;
	}
	if (base_cache.is_valid()) {
		return base_cache->get_property_default_value(p_property, r_value);
	}
#endif
	return false;
}
ScriptInstance *GDScript::instance_create(Object *p_this) {
	GDScript *top = this;
	while (top->_base) {
		top = top->_base;
	}
	if (top->native.is_valid()) {
		if (!ClassDB::is_parent_class(p_this->get_class_name(), top->native->get_name())) {
			if (EngineDebugger::is_active()) {
				GDScriptLanguage::get_singleton()->debug_break_parse(_get_debug_path(), 1, "Script inherits from native type '" + String(top->native->get_name()) + "', so it can't be assigned to an object of type: '" + p_this->get_class() + "'");
			}
			ERR_FAIL_V_MSG(nullptr, "Script inherits from native type '" + String(top->native->get_name()) + "', so it can't be assigned to an object of type '" + p_this->get_class() + "'" + ".");
		}
	}
	Callable::CallError unchecked_error;
	return _create_instance(nullptr, 0, p_this, Object::cast_to<RefCounted>(p_this) != nullptr, unchecked_error);
}
PlaceHolderScriptInstance *GDScript::placeholder_instance_create(Object *p_this) {