Unofficial Fallout 4 Patch

I've logged a support request with Bethesda, but I'm not holding my breath for a useful response.

Got response from Bethesda. Something along the lines of "given the issue has been widely reported, it's a safe bet the dev team is looking at it".

Certainly hope so, because I can't find anywhere he's referenced by something that could disable him in that way.

There are designer notes somewhere on that quest saying that this quest should become unavailable after the Institute has been destroyed.

i disagree that this storyline should disappear just because the institute gets destroyed, because synths continue to exist anyway without the institute, which means Dr Chambers's motivations wouldn't just disappear
this is a very weird decision from Bethesda to intentionally bug their own game and kneecap their own content they've put effort into
it happened to me, i beat the main story then started collecting settlements, but by the time i realized this happens my last valid save file is too far back, now Covenant makes no sense at all, the door guy acts like i've been there before. the Sewers/Compound would also make no sense to anybody who accidentally discovers it.
it would be pretty cool if UFO4P fixed this