I had something along those lines happen to me in my current game.
My Sovereign's offspring married into another faction's family fairly early on. That nation, shortly after the marriage, ceased to exist in a war with another NPC kingdom. This is well and good.
And then children happened!
Which was going to be better, until about half of my Sovereign's grandchildren decided to align themselves with the nation that no longer existed. So basically they stand at my capital city, unmoving, unanimated by any kind of AI, uncontrollable by me. In the dynasty screen, it even shows the proper line of succession for that kingdom! Except the AI seems to have been shut off permanently.
Now, it'd be pretty cool, I admit, if the kids, growing up, heard tales of from their mother of their glorious, now lost empire, and, upon growing to adulthood decided to strike out on their own and reclaim their birthright or somesuch. But it... doesn't seem to be working out that way! 
