I wrote the following and sent it to Bethesda support only to be responded to with an automated message giving me unhelpful advice and directions to post here. So here it goes.
"I am playing on PS4 and would like to know if there is any way to recover lost companions. So far I have lost Nick Valentine and X6-88. Nick was lost when I was clearing out Layton Towers. The two of us exited the apartment complex onto the roof and I dealt with the Raider leader up top. After the fight, I looked around and Nick had vanished. I have not seen him since. I never assigned him to a new area so he should have been staying at his detective agency, but no matter how many times I return he never does.
I lost X6 in a much less interesting way. I decided to work with another companion and sent him back to his default location, the SRB. When I returned to pick him back up he wasn't there. And so I wrote this out.
As I am on PS4 I can't simply spawn them in with console commands, and I can't think of any fixes to this. I have sat outside the SRB and waited for several days but he still has not reappeared. Nick has been gone for several real world days so waiting is clearly not an issue for him either. I guess the only thing I can do is to add to your feedback request for upcoming patches, and ask that you add some sort of item in every companion's default hub that will spawn them in place. Something like the bell in settlements that calls all of your settlers to it.
I hope this can be resolved as Nick was my favorite character and I would very much enjoy his return. X6 can come too."
Since then I have been made further upset by the addition of Cait's personal quest Benign Intervention not triggering. She will talk to me and set the quest up, but it never appears in my quest log and there is no way for me to advance further. I am unable to go back to an earlier save as I didn't realize the problem until after I had already gotten to the end of Vault 95, and all of my autosaves were used up getting there. My manual save was last made yesterday, but luckily I had a quicksave from the middle of the conversation, allowing me to break it off before a point of no return. I would appreciate some sort of fix for this in addition to the earlier problems. If possible.
However, this is now the third major problem I have with the game and to be honest I am fed up with it. I know that these are minor problems in the long run, but they are keeping me from being able to play the game as I want to, and that is unacceptable. I want to enjoy this game further but this whole situation is really bringing me down. I don't know what could be done to help, but anything would be appreciated.