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When it happened to me it boiled down to a faulty cable. Somehow shifting still worked, but the battery drained very quickly (either because the faulty cable prevented the charge or just by itself? No idea)
I replaced that one cable and everything was fine ever after.
It was the cable going from stem junction box to frame junction box and I think what did it was the bar bag constantly bending it and rubbing on it.
Anyone had their Di2 lose battery really quickly? Have felt I've had to charge way more than usual this year and really noticed it this weekend when I had at least 90% starting on Saturday and by Monday I was down to 25%. Common issue?