### 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
scr->clear();
		}
		s = s->next();
	}
	script_list.clear();
	function_list.clear();
	DEV_ASSERT(GDScript::func_ptrs_to_update_main_thread.rc == 1);
}
void GDScriptLanguage::profiling_start() {
#ifdef DEBUG_ENABLED
	MutexLock lock(this->mutex);
	SelfList<GDScriptFunction> *elem = function_list.first();
	while (elem) {
		elem->self()->profile.call_count.set(0);
		elem->self()->profile.self_time.set(0);
		elem->self()->profile.total_time.set(0);
		elem->self()->profile.frame_call_count.set(0);
		elem->self()->profile.frame_self_time.set(0);
		elem->self()->profile.frame_total_time.set(0);
		elem->self()->profile.last_frame_call_count = 0;
		elem->self()->profile.last_frame_self_time = 0;
		elem->self()->profile.last_frame_total_time = 0;
		elem = elem->next();
	}
	profiling = true;
#endif
}
void GDScriptLanguage::profiling_stop() {