I had an odd issue while riding today.  My Diverge has the Shimano Di2 1x, XTR rear.  I added a D-Fly (wireless unit) last fall when I picked up the bike.  I've been putting mile on the bike for months, no issue.  Raced Barry-Roubaix last weekend, no issues.  On todays ride, I intermittently could not shift.

After a few instances, I stopped and checked the connectors, all good.
I noticed the lights on the right bar end unit were blinking.  Green/Red.  This is pairing mode.  I pressed the button and rode on.
Issue came up again later, on a climb of course when I needed a new gear.  Later I lost all shifting and had to manually move the rear before/after climbs to get back to the start point.

Battery for unit was fully - fresh, charged.
On the ride, I checked connectors, even under the brake hoods.
I removed the D-Fly and still had no shifting.
When I got home, I connected the unit (without D-Fly, to a computer and ran the eTube software.  I updated the system - shifting returned.
I reconnected the D-Fly and used the paired phone to update its firmware.  Shifting is good.

I'm a little concerned about not knowing how or what caused the issue.

Any ideas?

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Do you have a seatpost battery? If so, could that connection or cable be faulty?  I would guess there is an intermittent connection issue, either from a connection or faulty cable.
Also, do you have blank plugs in all the open (unused) ports?
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In the this model, its not in the seat post, I hear its in the downtube area.  That said, the connections were good as ANT+ was connecting to the Garmin for most of the ride.  There are no open or unused ports.  The install does not use a junction box like I have seen elsewhere.  they used a split cable between the brakes. (no front derailuer.  
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I had a very similar issue happen to my Di2. Mine would completely drain the battery, and left me in one gear several times, that was after putting maybe 200 miles on a fresh charge. I swapped the battery, same thing, replaced some of the cables, same thing. Removed the d-fly unit, ran the battery for nearly 2000 miles. Put the d-fly back on, same lame crap. Got a new d-fly unit, and things have been great since.
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Battery Replaced, moved to seat tube as I took off the dropper post.
All cables replaced.
Removed D-Fly

Thought all was working, added a new inline Bluetooth connector to replace the front connector.  All 'seemed" ok.  Then tonight, it randomly has no shifting.  
I've plugged it into a charger, the charger does not come on, at all.

Right now it is unplugged.  One previous time after all was unplugged for about 2 hours, reconnected and it worked again.  

Still trying to figure this issue out.

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