If you take a master list unit, like an Elven Prince, in a theme list, like Twilight Kin, can you still take their army upgrade? In this case, can the Twilight Prince still take a hunting cat? I thought maybe it would swap army upgrades over to the theme’s ones, but can’t find anything to suggest that. (I’m actually surprised how little guidance on theme/master interaction there is in Uncharted.)
I guess the answer is yes. As nothing is said about it in the rules the units from the master list are transferred to the theme list as they are, including all their upgrades. In fact, I have wondered about the same when checking on the herd list where I believe the centaurs can still take the frenzied otter there.
Happy to know I’m at least not missing anything 
It does seem like they would have swapped army special upgrades when becoming theme units, but whatever I suppose.
Its not been categorically stated the the implication in a couple of comments in some threads on fanatics is - No, you can’t take a Master list units Army Special Upgrade unless the Theme army also has the same Army Special Upgrade.
In a TK list, any of the elf units from the Master list cannot take the hunting cat option (where available).
The section of the rules flagged up by Dan King was this bit
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I just found that in the main book! So basically for an Elven Prince in a Kin list to take a cat, the Prince’s entry would have to be reprinted in the Kin list with the cat in there? I think Free Dwarfs and stuff do this.
Yes, that’s my understanding.
The UE FAQ/errata isn’t out yet, which might clarify things