### 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
	MutexLock lock(this->mutex);
	profiling = false;
#endif
}
int GDScriptLanguage::profiling_get_accumulated_data(ProfilingInfo *p_info_arr, int p_info_max) {
	int current = 0;
#ifdef DEBUG_ENABLED
	MutexLock lock(this->mutex);
	SelfList<GDScriptFunction> *elem = function_list.first();
	while (elem) {
		if (current >= p_info_max) {
			break;
		}
		p_info_arr[current].call_count = elem->self()->profile.call_count.get();
		p_info_arr[current].self_time = elem->self()->profile.self_time.get();
		p_info_arr[current].total_time = elem->self()->profile.total_time.get();
		p_info_arr[current].signature = elem->self()->profile.signature;
		elem = elem->next();
		current++;
	}
#endif
	return current;
}
int GDScriptLanguage::profiling_get_frame_data(ProfilingInfo *p_info_arr, int p_info_max) {