### 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
String first = p_qualified_name.get_slice("::", 0);
	Vector<String> class_names;
	GDScript *result = nullptr;
	
	if (first.is_empty() || first == global_name) {
		class_names = p_qualified_name.split("::");
		result = this;
	} else if (p_qualified_name.begins_with(get_root_script()->path)) {
		
		class_names = p_qualified_name.trim_prefix(get_root_script()->path).split("::");
		result = get_root_script();
	} else if (HashMap<StringName, Ref<GDScript>>::Iterator E = subclasses.find(first)) {
		class_names = p_qualified_name.split("::");
		result = E->value.ptr();
	} else if (_owner != nullptr) {
		
		return _owner->find_class(p_qualified_name);