### 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 (p_script.is_valid()) {
		Ref<GDScript> gdscript = p_script;
		if (gdscript.is_valid()) {
			if (gdscript->get_local_name() != StringName()) {
				return gdscript->get_local_name();
			}
			return gdscript->get_fully_qualified_name().get_file();
		}
		if (p_script->get_global_name() != StringName()) {
			return p_script->get_global_name();
		} else if (!p_script->get_path().is_empty()) {
			return p_script->get_path().get_file();
		} else if (!p_script->get_name().is_empty()) {
			return p_script->get_name(); 
		}
	}
	return "<unknown script>";
}
#endif
GDScript::UpdatableFuncPtr GDScript::func_ptrs_to_update_main_thread;
thread_local GDScript::UpdatableFuncPtr *GDScript::func_ptrs_to_update_thread_local = nullptr;
GDScript::UpdatableFuncPtrElement GDScript::_add_func_ptr_to_update(GDScriptFunction **p_func_ptr_ptr) {