### 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 DEBUG_ENABLED
	print_verbose("GDScript: Reloading all scripts");
	List<Ref<GDScript>> scripts;
	{
		MutexLock lock(this->mutex);
		SelfList<GDScript> *elem = script_list.first();
		while (elem) {
			
			if (elem->self()->is_root_script() && elem->self()->get_path().is_resource_file()) {
				print_verbose("GDScript: Found: " + elem->self()->get_path());
				scripts.push_back(Ref<GDScript>(elem->self())); 
			}
			elem = elem->next();
		}
	}
	
	scripts.sort_custom<GDScriptDepSort>(); 
	for (Ref<GDScript> &scr : scripts) {
		print_verbose("GDScript: Reloading: " + scr->get_path());
		scr->load_source_code(scr->get_path());
		scr->reload(true);
	}
#endif
}
void GDScriptLanguage::reload_tool_script(const Ref<Script> &p_script, bool p_soft_reload) {