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So I tried the app for the first time today and when I first went to do the rear derailleur maintenance it was in the +3 micro shift position. After a bit of fine tuning it’s ended up in -11 and this has solved the shifting problem. It now happily moves up into the large cog and with the limit screw set properly no longer throws the chain in the smallest. Weird perhaps the position of the derailleur hanger is just slightly outboard on this bike? Anyway thanks for the advice!
Sounds like you may have maxed out on the micro adjust in the outboard direction.
If not then a simple answer is to plug into etube and reprogramme the rear derailleur. Pretty sure you can still do this with your charging cable.