What did Zeno destroy? I'm confused about what Zeno destroyed for killing Zamasu, did he destroy just the Earth, the entire Universe, or the 12 universes?
I'm assuming your referring to episode 67. Zeno said the following:


  A world like this must be destroyed.





  I believe it safe to assume that the earth was destroyed but not the
  entire universe. If Zeno did destroy the entire universe there
  wouldn't have been a way to use the time machine to go back and get
  him because time is a component of a universe. No universe, no time,
  no travel by time machine.




The above was my original answer to this question until I read chapter 18 of the manga and Whis said the following below. 



Based off of this and prior knowledge we received in the anime that the King of All has destroyed universes before. I now believe it is safe to say that he actually destroyed the entire Universe in that timeline. 

Previously I argued that if a Universe doesn't exist time can't exist either. And this is stepping away from anime for a bit but physics tells us that 


  Matter cannot be created or destroyed only transformed 


So in summation after a little research I've come to a different conclusion. 

Even if existence as we define it comes to an end. Time does not, we may lose the capacity to quantify or comphrehend it but time is everpresent.

I can honestly believe that this is a valid answer.