I don't know how quickly that's going to change, if ever, unfortunately. There's no part of the world where they can update the game where someone isn't supposed to be sleeping.

I will mention that I would love to see something that remembered I was doing autos and resume them after an update, as I am never awake for them myself.

I would say it's far more annoying when there's a temporary loss of internet during multi-battling while being AFK. Even after it comes back, it just keeps showing that "Re-login/ Retry" menu like it's some Universe-altering dilemma and the game needs my written approval, signed in triplicate: YES! RETRY!  Should've put a timer on it.

With updates you can still roughly know when they are coming so it gives you time to prepare.

I thought auto battles ended because my pc reached its sleep cycle timeout.  

That could also cause a disruption, but you can turn that off on your computer, if you'd like.