And where is answer for the quesstion?
I have the same problem.
After I assigned companion like minister and then lose the city it disappeared. Loose couple of compnaious this way. And even more after.
When someone leaves you due to low moral they also gone. 600+ days after Ymira left the band and didn't come back to Calradia. Only 5 companies left in my game.
I tried cheats and teleport across all Calradia. Maybe they just do not appear in Travelers list or something. But no. They just gone.
Vanilla. No mods.
