mmmh... Could it be that there were some independence wars running at the same time? If the emperor had lost one, the CA would have been automatically lowered, but the "Lower CA" war would have kept going as it started before the change in CA. I never seen it happen but I guess it is how it could be. However I agree that, if the CA has been lowered by other means, then the Lower CA War should end inconclusively.
Interestingly I had posted a Bad Luck Brian meme some time ago on the exact same topic

(Autonomous vassal kingdom: Vassals plot lower CA)