"Wait, even though he has ascended, he's now merely the head of the Spy Bureau. I'm the Commander-in-Chief at the frontline, how can he order me? We're equal!" Qing Yu said, "So far, I only take orders from the Family Head."
It's not that Qing Yu can't see the situation, nor that he doesn't recognize Qing Chen.
However, the consortium and the army aren't child's play. Even if you are the Crown Prince, you can't command all the troops, and you might not even command the National Policy Advisors within the Qing's Family.
Currently, Qing's Family hasn't even confirmed the Shadow.
Everyone pledges their allegiance as a symbolic gesture, but it doesn't mean they lower their status.
Until the Family Head abdicates, the Crown Prince is only the Crown Prince, that's all.
It's not that Qing Yu isn't loyal, but that's the rule, otherwise, everything would be chaotic.