Yeah - some of the dialogue made it seem that this was almost a "first meeting," while other bits didn't. It was just very odd, especially how Jor-El was left by Jurgens (being taken away in that vortex thing and Clark saying he'd find out what happened to him, iirc). And I've been very much enjoying the books, so far.
I didn't think about Henshaw, but that's a good point - if the Fortress is destroyed, what happens with him? Or will he even be addressed, might be a better question.