If you're coming back with this patch and are trying to play a historical Leader/Civ combo across all ages and expect the AI to do the same make sure you set up your game properly
Note, this is based on the beta and it could have been changed.
First in advanced options set AI civs to historical. Second, switch from the mirror option which is on by default to AI Civs never switch.
With the mirror option enabled:
If you play with an antiquity civ, AI leaders will be associated with an apex civ in antiquity and remain like that for the whole game.
If you play with an exploration civ they will switch to apex civs in explo and stay like that in modern.
If you play with a modern civ they will switch in modern.
This is because the mirror option switches when you reach an apex age regardless of you deciding switching civs and this has interesting consequences. A quick example would be you playing as Pachacuti of the Incas against Ada of England and Napoleon of France in antiquity. When you hit exploration and keep the Incas one of them will turn into Normans and the other one into another apex civ and they will remain like this until the end of the game unless you switch civs in modern in which case they will become England and France again.
Once again, this is based on the beta and I'm not sure what will be in the update tomorrow but make sure you check the tooltips when setting up your game. If you want to try setting up a game where all leaders keep their associated historical civs from start to finish double check the mirror option because it doesn't exactly work as people claim it does on this subreddit.
EDIT: I can confirm it works differently now.
Set up a game as Pachacuti, found Bolivar of Mexico and 15 minutes of shift+enter later he's now still Mexico. However there's a weird bug because if you shift+enter on the last turn before selecting your civ he turns into Bolivar of Ming.