There are endless "what if" type scenarios where the answer boils down to simply detecting that this is one of those "what if" scenarios and then initiating the appropriate emergency procedure so it can be figured out properly. E.g. an emergency landing is always an option.
That's basically what pilots do as well. They spent most of their time assessing whether everything is OK via checklists and when it is somehow not OK there's not enough time to think and they reach for some emergency procedure instead. Mostly this never happens and there are whole sets of procedures that most pilots never even handle outside a simulator. E.g. landing a 737 with all engines out is a thing but obviously not something most 737 pilots would ever have to do in a real plane.
ATC obviously needs to be automated too. Automating routine interactions like exchanging altimeter settings, agreeing on what the current weather report is, what the active runway is, etc, would eliminate a lot of need for humans to talk to each other and pass the information on to dedicated computer systems on both ends (which is largely what pilots and controllers do). These systems could, and should, communicate directly. Any autonomous plane would have to be integrated this way. Situational awareness is currently bottle necked on the ability to pass information around, which happens to be something computers are good at.
A stop gap solution is putting a remote human pilot in between to enter information relayed by human atc. The main challenge is not just replacing the pilots but also ATC and standardizing the interactions between them.