### 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
{
		HashMap<StringName, GDScript::MemberInfo>::Iterator E = script->member_indices.find(p_name);
		if (E) {
			const GDScript::MemberInfo *member = &E->value;
			Variant value = p_value;
			if (member->data_type.has_type && !member->data_type.is_type(value)) {
				const Variant *args = &p_value;
				Callable::CallError err;
				Variant::construct(member->data_type.builtin_type, value, &args, 1, err);
				if (err.error != Callable::CallError::CALL_OK || !member->data_type.is_type(value)) {
					return false;
				}
			}
			if (member->setter) {
				const Variant *args = &value;
				Callable::CallError err;
				callp(member->setter, &args, 1, err);
				return err.error == Callable::CallError::CALL_OK;
			} else {
				members.write[member->index] = value;
				return true;
			}
		}
	}
	GDScript *sptr = script.ptr();