Same issues here since the latest update on my 6S in my ’15 Wrangler Sport, even while testing all the betas I never ran into this issue. I’ve noticed that if you’re connected via USB and try to utilize the bluetooth, wether it be for streaming audio, or doing handsfree calling you’ll run into the issues. It seems the head unit (ever since the latest update for some odd reason) has become extremely particular how it lets you use the bluetooth. Happened to me today actually, was streaming audio through a usb connection and had to take a call and it dropped my call back to the headset and disconnected my bluetooth altogether.
If you stream all audio via bluetooth, you more than likely won’t have anymore issues. But if you want a direct connection through the cable, then you’re more than likely going to be SOL using bluetooth for anything. If you use a direct connection and have your notifications turned on it won’t even sound unless you’re using bluetooth. I use an Escort Radar application while driving, and unless I’m using bluetooth I won’t hear any notifications of speed traps/live police alerts come through. Just subdued audio for the duration of where the chime should’ve been.
And as far as certain apps only using bluetooth and nothing else, I actually had the same issue using Spotify in my last Chevy truck. I wanted a direct connection, but it would only play via bluetooth. So I cancelled my subscription and went back to Apple Music because it played how I wanted it to when connected. This may help some of you, and it may not. Either way, best of luck.