### 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
#ifdef TOOLS_ENABLED
	return valid && (tool || ScriptServer::is_scripting_enabled());
#else
	return valid;
#endif
}
Ref<Script> GDScript::get_base_script() const {
	if (_base) {
		return Ref<GDScript>(_base);
	} else {
		return Ref<Script>();
	}
}
StringName GDScript::get_global_name() const {
	return global_name;
}
StringName GDScript::get_instance_base_type() const {
	if (native.is_valid()) {
		return native->get_name();
	}
	if (base.is_valid() && base->is_valid()) {
		return base->get_instance_base_type();
	}
	return StringName();
}
struct _GDScriptMemberSort {
	int index = 0;
	StringName name;
	_FORCE_INLINE_ bool operator<(const _GDScriptMemberSort &p_member) const { return index < p_member.index; }