Yea, I believe Istriya has been replaced since weve met her. And, I tend to think your earlier assessment that Skeaös was replaced right before Conphas came back from Kiyuth, to be accurate. From that point on he is no longer in agreement with everything Xerius says and wants. Here in Chapter 7 its evident, because he didn't agree with giving up the Vulgar HW. Why Not? Its what's best for the Empire, Conphas see's the brilliance in it. No, he's a Skin-Spy, and wants nothing short of making it to Shimeh and the Cishaurim. But, as you say, its very evident in the next chapter.
ETA: ahhhhhh, you're right. After reading your quote again, Skeaös was in agreement with Xerius. Xerius was lying about that, never caught that.