So my CarPlay keeps dying at random. Thought it was a cable issue but nope, changing that fixes nothing. Only way to bring it back is to reboot the radio. Luckily since the 4000 screen comes off it is a quick reboot for me.

It happened with my old iPhone 5s and now it's happening with my 6s+. I'm on the latest software all around, and when it happens it's a toss up of if Bluetooth will kick in to be a backup. The machine still recognizes that something is plugged into USB, so it won't let Bluetooth stay on for music sometimes, but the iPod menu dies for both ports and CarPlay won't relaunch even if I unplug and plug the phone back in. Blah

My nex 4000 (with iphone 6) does the same thing, though not that often.  I think it's a head unit issue becuase like you said, unplugging and replugging (even rebooting the phone) doesnt fix it.

In general the whole Carplay program is buggy and kinda annoying.  Im a HUGE apple fan, if apple makes it i own it, but Carplay seems to be neglected by apple and perhaps doesnt get the funding it needs to make the program work the way all apple products do- flawlessly.  

I think this is the reason car manufacturers are hesitant putting this in place too....

I had the same problem with my 8100.  I was able to correct the issue by disabling the following settings on the Iphone:

Disable: General>>Handoff & Suggested Apps>>Handoff

Disable: General>>Handoff&Suggested Apps>>Suggested Apps>>Installed Apps

I also have Bluetooth Audio disabled, but you may or may not need to disable it.  I just don't use it.

The connection to CarPlay has been pretty stable since disabling these settings.

Configuration:

Pioneer Firmware: 1.03

IPhone 6: 9.0.2

Yeah that didn't work sadly.

I had the same problem with my 8100.  I was able to correct the issue by disabling the following settings on the Iphone:

 

Disable: General>>Handoff & Suggested Apps>>Handoff

Disable: General>>Handoff&Suggested Apps>>Suggested Apps>>Installed Apps

 

I also have Bluetooth Audio disabled, but you may or may not need to disable it.  I just don't use it.

 

The connection to CarPlay has been pretty stable since disabling these settings.

 

Configuration:

 

Pioneer Firmware: 1.03

IPhone 6: 9.0.2

Ok, it may be premature and may jinx myself, but so far, so good!  It is the longest this unit has worked for a few days.  I did everything in this list.  I'm putting it through it's paces and trying to make it crash...so far nothing.  Fingers crossed.

Worked all day without any major hiccups.  Still not completely convinced though.

Found the problem. It was the cable. Make sure to use a true Made for iPhone cable and to make sure it has no bells and whistles like some of those ones that light up or in my case use a lightning extension cable.

Oh man!  Hopefully this will help me too.

I skimmed over this thread when posting mine simply because the title was 4000.  I already have a genuine lightning cord and I just disabled the functions listed here. 

Don't want to jinx myself either, but so far so good here, too.  I changed from HD radio to iphone music & then cd player.  Got out to go in a convenience store, got back in & plugged the phone in without any special handling & it worked automatically.

JCSoldier, if you're a drinking man, I'd be willing to send you a bottle of Goose, Crown, whatever.