I have one solution for this and one additional statement to follow. So instead of vanashing perhaps Larian could look into adding a bonus fight at your camp the next time you go back to it after finishing act 1, which is where you left them RP wise, and when you go back they all the ones not in your party just so happened to turn into mindflayers. Would this make it feel better than them just vanishing.
My statement would be how often are we actually making party changes. I know for me once i have a group together I really don't bother to make changes unless the story dictates such as needing Gythraki (however its spelled) lady to talk to Zorru(or whatever his name is). Maybe this is just me and if that is the case i completely understand where your coming from as to why it would be such a big game changer for them to just vanish.
