### 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_NULL(p_func_ptr_element.element);
	ERR_FAIL_NULL(p_func_ptr_element.func_ptr);
	MutexLock lock(p_func_ptr_element.func_ptr->mutex);
	p_func_ptr_element.element->erase();
}
void GDScript::_fixup_thread_function_bookkeeping() {
	
	
	DEV_ASSERT(!Thread::is_main_thread());
	MutexLock lock(func_ptrs_to_update_main_thread.mutex);
	MutexLock lock2(func_ptrs_to_update_thread_local->mutex);
	while (!func_ptrs_to_update_thread_local->ptrs.is_empty()) {
		List<GDScriptFunction **>::Element *E = func_ptrs_to_update_thread_local->ptrs.front();
		E->transfer_to_back(&func_ptrs_to_update_main_thread.ptrs);
		func_ptrs_to_update_thread_local->transferred = true;
	}
}
void GDScript::clear(ClearData *p_clear_data) {