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+1
If your di2 shifting gets a bit wonky, it's almost always a bent hanger. Once you have the indexing and limit screws set up properly they will always be good because there are no cables to stretch, the derailleur always shifts the same distance and the rear spacing/spacing between cogs doesn't change.If a hanger alignment doesn't fix it the only other thing that causes issues is a gunked up/worn tension spring which will affect how your derailleur moves as you shift up and down the cassette. Easy to pull it apart to check and replace if needed.
Yeah, but is it? Di2 just just suddenly shift different amounts so the only reasonable explanation is something has moved and the most likely culprit is usually the hanger (or loose cassette, or worn chain, but you addressed one of those issues).
I've never updated firmware on any of my Di2 and they all just work. If it was the extremity cogs I'd suggest your limit screws were off but because it's kinda in the middle of the cassette it does sound more like something is piss.