I too have had some annoying issues with my 2016 Civic EX. Although I have had it to the dealership twice, the permanent fix doesn't exist, at least for me. Here's what has happened to me too many times to remember: We pair our phones up to the system, and everything works fine, including Android Auto. Then for no reason whatsoever, I will get in the car with my Bluetooth on, and the system doesn't recognise my phone or my wife's phone. The record without this happening is 19 days. The ONLY fix for me is to do a factory data reset, which takes about 5 minutes. After I do that, the system is like it was on day one, and I have to re-pair our cell phones, and off we go again, UNTIL the next RANDOM time I get in the car with my Bluetooth on, and the system doesn't recognise my phone.
To do a factory data reset, go to settings, system, scroll all the way down and touch Factory Data Reset and touch "YES" or "OK" about 4 times and don't turn your car off until the system comes back on. The 1st time you do this, it may scare the crap out of you, but it does work.
Hopefully, Honda will have a software update to address this at some point.