I am level 63 on my second play through and chose the Brotherhood ending.
Now I am tidying up loose ends, maxing companions and improving settlements but I left a few of the bigger side quests until now.
I walked to Covenent, which is now open to me even though I have never taken the SAFE test, but Honest Dan is nowhere to be found. I went across the water to the "facility" and they are cordial but will not let me past the inner door.
Moved on to the USS Constitution and met the Captain but the quest stalls there with no further goals in the pip boy.
Next I went to Cabot house and rang the bell, but they told me to get lost. I have not tried to find the family Merc, Ed Deegan who hired me in my first playthough so this one may not be stalled.
My question is: Do a large number of quests stop working after the "ending" of the game even if they are not associated with a major faction that is gone? (In this case the Institute and Railroad are kaput.)