Underground Undercover - Can't warn Desdemona

I'm trying to liberate as many synths from the Institute as possible before I burn it to the ground. That means completing the 'Underground Undercover' quest, which basically goes into hibernation and requires you to fight on behalf of the Institute through several missions, one of which forces you to become enemies with the Brotherhood of Steel.

When that happened, the first thing I did after completing the related mission was to fast-travel to the Prydwen to see if I could take out an entire airship full of guys in power-armor (and because how dare they turn hostile on me in the first place?). That operation went well enough, and eventually the 'Underground Undercover' quest resumed. It wants me to warn Desdemona of an imminent Brotherhood attack.

The problem is, it won't let me. Attempting to speak with her just gives a generic chit-chat response, and doesn't advance the quest. There's some further documentation of the issue here. So what I've got in my game is:

1. Glory is alive.
2. Most BoS members on the airship are dead.
3. Most BoS members on the ground at the airport are alive (I sniped a few from the airship).
4. Paladin Danse is dead (he attacked me when I went back to Sanctuary to drop off some crafting supplies).
5. The 'Underground Undercover' quest wants me to warn Desdemona.
6. I haven't progressed the 'End of the Line' quest past the point where it wants me to talk to Father (though I tried that, and it doesn't help anyways).

...and it's basically stuck there. Does anyone know of a way to get the 'Underground Undercover' quest to progress? I don't want to pick a fight with the Institute until I've rescued the synths (so workarounds along the lines of 'just go kill some Institute people' won't quite work).

Or failing that, does anyone have the console commands that will resurrect all of the BoS members on the airship (I'm hoping that maybe putting them all back will unbreak the game)?

The closest I found to a workaround for this issue was to reload an old save, from before I had manually attacked the Prydwen. After doing that, I found the Underground Undercover quest progressed correctly with the following in-game state:

1. Glory is alive.
2. BoS members on the airship are alive.
3. BoS members on the ground at the airport are alive.
4. Paladin Danse is dead.
5. The 'Underground Undercover' quest wants me to warn Desdemona.
6. I haven't progressed the 'End of the Line' quest past the point where it wants me to talk to Father.

After that my game worked as it should (got to fight off the BoS attack, got the mission to attack the Prydwen, looted Final Judgement off of Maxson's corpse, was able to warn Desdemona again after talking to Father, etc.).

Another interesting thing I found was that if you progress Underground Undercover to the point where it wants you to clear the control room, you can instead turn around and take the elevator back into the Institute proper and pick a fight with everyone without getting banished. Among other things, that lets you take out members of the directorate and other named Institute NPC's who disappear if you just keep progressing Underground Undercover.