Wondering if you could elaborate on that? I know I saw someone mention something about his high charisma messing with the NPC's or something and i don't quite understand it as I haven't noticed anything.
At any rate, you could just toss him out of the party before an influence encounter.
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I missed certain influence markers on Dxun, for example. Like the stranded Mandolorian. After the marker, bao-Dur remained silent, while the Disciple spouted off something or another. And that's one of Baos markers. There was another point where I had the two of them together, and once again Bao was silent when he should have had a new dialouge option. Instead Disciple opened up his yap and I said something mean that made me lose influence with Bao even though I wasn't talking to him and somehow Atton gained influence even though he was back on the Ebon Hawk. And after that I did swap out party members before the influence markers.