### 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
_base = nullptr;
				ERR_FAIL_V_MSG(false, "Cyclic inheritance in script class.");
			}
		}
		if (base_cache->_update_exports(r_err, true)) {
			if (r_err && *r_err) {
				return false;
			}
			changed = true;
		}
	}
	if ((changed || p_instance_to_update) && placeholders.size()) { 
		
		HashMap<StringName, Variant> values;
		List<PropertyInfo> propnames;
		_update_exports_values(values, propnames);
		if (changed) {
			for (PlaceHolderScriptInstance *E : placeholders) {
				E->update(propnames, values);
			}
		} else {
			p_instance_to_update->update(propnames, values);
		}
	}
	return changed;
#else
	return false;
#endif
}
void GDScript::update_exports() {