### 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
r_ret = const_cast<GDScript *>(this)->callp(E->value.getter, nullptr, 0, ce);
					return true;
				}
				r_ret = top->static_variables[E->value.index];
				return true;
			}
		}
		{
			HashMap<StringName, GDScriptFunction *>::ConstIterator E = top->member_functions.find(p_name);
			if (E && E->value->is_static()) {
				if (top->rpc_config.has(p_name)) {
					r_ret = Callable(memnew(GDScriptRPCCallable(const_cast<GDScript *>(top), E->key)));
				} else {
					r_ret = Callable(const_cast<GDScript *>(top), E->key);
				}
				return true;
			}
		}
		{
			HashMap<StringName, Ref<GDScript>>::ConstIterator E = top->subclasses.find(p_name);
			if (E) {
				r_ret = E->value;
				return true;
			}
		}
		top = top->_base;
	}
	return false;
}
bool GDScript::_set(const StringName &p_name, const Variant &p_value) {