[sanghill]

Is your Autel scanner reading FCA codes correctly? I am asking because my old scanner doesn't read codes on the Cherokee, works fine on my Oldsmobile though.
Maybe get a free scan someplace? Just wondering.
I vote for checking the battery connections one more time. Make sure they won't twist. Well, since you had the same problem pre new battery that probably means it isn't it.
I have a 2014 V6 TH and haven't had that problem yet.

 

[sanghill]

See if this helps: Key fob won't lock/unlock doors Post #4.
Watch the video.
Done correctly shouldn't cause any problems, might even work.