Enkidoh's got it, Zenos' body was dead in the original timeline anyway, even if his soul was still around. Also keep in mind that Zenos' return had absolutely nothing to do with Black Rose, aside from him turning up at roughly the same time as Gaius and Estinien on their disposal mission. He mostly didn't actually care about it, we can only assume how he would've responded to it if it was still in play when he took the throne.

I'm torn on if he'd order it destroyed because it'd be a dishonorable death compared to Glorious Combat, or if he'd crack it out to kill Ishgard or something just to make people mad enough at him to fight him harder.