Yamato was overpowered and humiliated by Kaidou on the roof, Kaidou for X reasons stopped focusing on Yamato (things ended very badly for Yamato if he decided to continue), and then she got up saying that it wasn't over yet when Kaido got out of his form hybrid and went into its Base form for no reason.
Kaido's return to his Base form symbolizes to me that he ended up with Yamato, that's how I see it, then Yamato only served in the fight with Kaidou for a combined blow with Luffy, and that's it. Regardless of what you think about Kaidou vs Yamato, even under the circumstances that Kaidou was up against Yamato (already showing signs of exhaustion) Yamato declared that he couldn't defeat him.