Well, he noticed that Lithor was absent, so he is making assumptions based on his...not liking Lithor.
But in that case (that Thornden would probably speak up), perhaps it would be best for Coen to kinda give Thornden a look to encourage him to speak up (whether or not that's necessary), and Thornden can say what he knows.
That could be what the look is between them that is interpreted by Athanar as them not knowing if they were dismissed...
We might have to ask
Legate to edit or place your/my post ahead of his, though, since he has written that Coen and Thornden are heading towards Hilderinc and Aflorgaed. :\ Not that it's a huge deal.