### 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
ERR_FAIL_COND(!named_globals.has(p_name));
	named_globals.erase(p_name);
}
void GDScriptLanguage::thread_enter() {
	GDScript::func_ptrs_to_update_thread_local = memnew(GDScript::UpdatableFuncPtr);
}
void GDScriptLanguage::thread_exit() {
	
	
	if (!GDScript::func_ptrs_to_update_thread_local) {
		return;
	}
	GDScript::_fixup_thread_function_bookkeeping();
	bool destroy = false;
	{
		MutexLock lock(GDScript::func_ptrs_to_update_thread_local->mutex);
		DEV_ASSERT(GDScript::func_ptrs_to_update_thread_local->rc != 0);
		GDScript::func_ptrs_to_update_thread_local->rc--;
		if (GDScript::func_ptrs_to_update_thread_local->rc == 0) {
			destroy = true;
		}
	}
	if (destroy) {
		memdelete(GDScript::func_ptrs_to_update_thread_local);
	}
}
void GDScriptLanguage::init() {