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2 comments
Possibly a dodgy cable? Being intermittent suggests minor damage somewhere so maybe get a testing Di2 cable and try connecting the battery to the junction box (might not be easy for internal cables) using that to see if the problem persists.
Update - resolved!
I finally found a mechanic willing to take the time to troubleshoot it with me as well as to call Shimano to explain the situation to them and get their input. Based on what I'd already tried (replacing junction A, isolating each lever, etc.) we all agreed that the next best candidate was junction B. Luckily that's an inexpensive part, although difficult to get to – I was happy to have a shop to open the bottom bracket for that. Anyway, we swapped it out, put it all back together and voila, it seems to be fixed.
Thanks for everyone's help and input!