I've been fighting with the Di2 on my 2 year old Cervelo R3 for several weeks now and so far Di2 seems to be winning. In the middle of a ride a few weeks back it just started to respond only intermittently. At first the rear derailleur stopped responding but the front would still shift. That's opposite from the behavior when the battery runs low, and I had recently charged it, so it obviously wasn't a dead battery. If I stopped it would shift for me, but it gradually got worse. Eventually the front stopped responding too.
I don't have any other experience with Di2, but it's an electrical system with sealed components so the problem has to be with one of the cables or one the components. It almost always works when the bike is up on a stand. Riding with hands on the hoods often caused failure, so that pointed to the brake lever being the issue, which still seems to me the most likely culprit. I've tried riding with the brake hood pulled back and fiddling with the connection, and that sometimes worked. In fact, I replaced my junction A with a display unit that's meant for mountain bikes and you can see the screen flicker on and off when fiddling with that connection.
So that seemed to tell me I should try replacing the right brake lever. But I wanted to test the hypothesis first. In theory, if I removed the right shifter from the system and kept only the left shifter attached, it should work fine and only be able to shift the front derailleur. That would eliminate what I had diagnosed as a short or bad connection in the right lever. But when I did that, the left lever started behaving the same – only shifting intermittently and I could see the display flicker on and off. I find it hard to believe that both levers could have started failing in this same way at the same time, so maybe that is pointing to something else?
Di2 components are not exactly cheap, so I don't really want to just start swapping out components without understanding what's actually wrong. The last shop I brought it to said they opened the bottom bracket and replaced the cable between junctions A and B. I've replaced the cables between junction A and both levers. It's now been taken apart, diagnosed on the eTube software and put back together 4 times by me and 2 different shops, each time with the same result – testing it on the stand and riding around the block a few times it seems fine, but a few miles into my next ride it stops responding again.
I'm pretty much about to tear my hair out or ditch the bike at this point. If anyone has experience with Di2 and could offer any ideas, I'd be happy to hear them.
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