I just encountered this to. After talking to eothas in ashen maw im reuinted with my soul. When i meet my soul it asks me "are you the same watcher who returned the dyrford souls to theyre intended bodies?" (the poe1 icon also appears). Problem is, im not. I didnt chose the Hylea ending, i chose the Berath one. A response that requires 2 benevolent and 1 passionate dispositions is also greyed out for some reason, even though im maxed out in both those dispositions.
I really hope this gets fixed in next patch. I just wanna finish this playthrough before the DLCs arrive.