At the moment, Yates' own bid to become Britain's first-ever winner of the Giro d'Italia is firmly on track. And, indeed, on the same stage that the Lancashire racer overtook Mark Cavendish to become the British rider who has spent most days in pink - five - Yates even snatched a three-second time bonus at an intermediate sprint.
But Yates' achievements on Tuesday were overshadowed almost completely by the disastrous day for Chaves - who finished in the gruppetto some 25 minutes down after being dropped on the first climb. The consequences of Chaves' tough ride are far from insignificant for Yates, too.
"I think it becomes harder for me because when we were on the final climbs before, we had two cards to play, it was much more difficult for our rivals to chase us both," Yates reasoned after the stage. "But now it's only me, and we'll have to adjust."
The only silver lining to the Chaves-shaped GC cloud, Yates said, was that "for sure he'll be a strong help for me in the climbs, so you can look at it two ways.
"[But] We will have to adjust our tactics, and I'm very disappointed for him."
Yates echoed team manager Matt White's words that there had been no indication such a bad day at the office was looming for Chaves.
"We had had a good rest day, we were relaxed, and from what I saw he was his normal self. But you can see it with other riders after a rest day, it was one of those moments, and he didn't have enough power in the legs."
It had been, Yates said, an extremely difficult day's racing right from the gun. "For sure it was one of the most aggressive starts I've seen for a while, especially for such a long stage. It was the same as if it was a 100-kilometre stage. It was really ferocious. We just never stopped, it was a very difficult day for everybody."
Chaves, though, suffered the most difficult day of all the GC contenders, even though Yates' confidence in himself remains at a high. But he said he was anything but complacent about what was coming up.
"I'm sure I'm going well, I have great legs. But I'm never going to think this is going to be easy. My rivals are extremely strong. So I'm self-confident, but I understand what I try to achieve."
The final week of the Giro d'Italia, he insisted, was not something he found particularly daunting. "But I am scared of the [stage 16] time trial. I'm going to need a lot of time. Today I gained three seconds, and if I can continue to keep getting little bits here and there, then I'll be happy."
Wednesday's rugged trek through eastern Italy includes some climbs where his brother, Adam, tackled en route to victory on a stage of Tirreno-Adriatico, and Yates said he would be calling him up to contact him about it.
As for how the team rethinks their strategy following Chaves' disappearance from the GC battle, though, that may well take longer to be decided.