Here is my current save with the issue: https://www17.zippyshare.com/v/ixwVYWcm/file.html
I can select Aloth on the manage party screen, but he isn't added once I've accepted (which I believe has been happening ever since the merchant ship encounter on your way to Ori o Koīki for The Painted Masks quest).
Is there a console command that could help other than ManageParty?
I am also having this problem, but specifically with Aloth. His companion quest and place in the party roster are still there, but I am unable to recruit him to my current party and he is no longer on my ship. Please fix soon!
Does anyone know about the console command for DispositionAddPoints? The formula is DispositionAddPoints dispositionGuid strengthGuid. The problem is that "shady" or "clever" are not valid game data objects, and neither is "disposition_clever" or "disposition_shady"