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.
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?
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.
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.
Update: 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.