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I'd say.... save her next time. It's unfortunate, but if you don't have a save from before that, it's likely that anything else you might do (particularly 'removing and replacing files'...) will probably mess up the game further.
Is it possible that you'd wandered too close to the greenhouse? Did you turn on the sprinklers in it or anything at all? Because generally that will alert the telepath, and it might have led to her dying. You can't get too close to the people being controlled, because their heads will explode...
I wonder, do you have the audio log basically telling you about her / get a message to help her? Maybe that's one of the triggers to have them up and around, and otherwise they'd just be dead?
I had a quest bugging out (Mikhailas Father Quest) in my first playthrough and no matter how far I'd went back in savefiles, the Quest was still broken. I had no problems with this quest or any other quests on my second playthrough with a new campaign savefile though.
I think stuff like this has something to do with the world/simulationbuilding and it seems like this is done on the first load of a new campaign. I'd say this quest is just lost for you.
Maybe something is just wrong with your game install? Try having steam scan the files. Because there are numerous people here who have not experienced this yet, but are throwing out lots of ideas.