### 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
Object *owner = nullptr;
	GDScript *_baseptr = this;
	while (_baseptr->_base) {
		_baseptr = _baseptr->_base;
	}
	ERR_FAIL_COND_V(_baseptr->native.is_null(), Variant());
	if (_baseptr->native.ptr()) {
		owner = _baseptr->native->instantiate();
	} else {
		owner = memnew(RefCounted); 
	}
	ERR_FAIL_NULL_V_MSG(owner, Variant(), "Can't inherit from a virtual class.");
	RefCounted *r = Object::cast_to<RefCounted>(owner);
	if (r) {
		ref = Ref<RefCounted>(r);
	}
	GDScriptInstance *instance = _create_instance(p_args, p_argcount, owner, r != nullptr, r_error);
	if (!instance) {
		if (ref.is_null()) {
			memdelete(owner); 
		}
		return Variant();
	}
	if (ref.is_valid()) {
		return ref;
	} else {
		return owner;
	}
}
bool GDScript::can_instantiate() const {