I can't help but think Nine's behavior has something to do with story trying to exert it's power again. Like it's in line for him to be a worrywart but not to this extent imo.
The funny thing is, What if, this is just another loop for Yuri and after this, next loop, Melissa returns to be the original personality (not the modern day knowledge one). That's a massive torture to her after getting a glimpse of hope....