### 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
return OK;
	}
#endif
	{
		String source_path = path;
		if (source_path.is_empty()) {
			source_path = get_path();
		}
		Ref<GDScript> cached_script = GDScriptCache::get_cached_script(source_path);
		if (!source_path.is_empty() && cached_script.is_null()) {
			MutexLock lock(GDScriptCache::singleton->mutex);
			GDScriptCache::singleton->shallow_gdscript_cache[source_path] = Ref<GDScript>(this);
		}
	}
	bool can_run = ScriptServer::is_scripting_enabled() || is_tool();
#ifdef TOOLS_ENABLED
	if (p_keep_state && can_run && is_valid()) {
		_save_old_static_data();
	}
#endif
	valid = false;
	GDScriptParser parser;
	Error err = parser.parse(source, path, false);
	if (err) {
		if (EngineDebugger::is_active()) {
			GDScriptLanguage::get_singleton()->debug_break_parse(_get_debug_path(), parser.get_errors().front()->get().line, "Parser Error: " + parser.get_errors().front()->get().message);
		}
		
		_err_print_error("GDScript::reload", path.is_empty() ? "built-in" : (const char *)path.utf8().get_data(), parser.get_errors().front()->get().line, ("Parse Error: " + parser.get_errors().front()->get().message).utf8().get_data(), false, ERR_HANDLER_SCRIPT);
		reloading = false;