I have killed the BOS. Father just gave me a quest to go kill Desdemona. I had the option to kill her or warn her. I don't want to kill her I want to side with the railroad. She won't talk to me, if I interact with her she just says some default line. Bug?

it's a bug , u're best bet is to reload an older save

out of curiosity , why did u side with the Railroad ?

You're almost "railroaded" (ha!) into joining the Railroad as they are presented as mysterious "saviour" group that's the last line of defense against the eeeeevil Institute. It's only after you get to know all the factions that you might decide that the Railroad are not worth supporting.

Is the quest to help "Patriot" still available? If so then you may have one more option to eradicate a better future for man kind for a few synths that may not even remember anything. Though I am uncertain, I imagine that quest should still be there as I had that option open before I reluctantly butchered the Railroad. I didn't mind taking out Des, just Tinker Tom and the others did not deserve that fate given the trust they put in my only survivor. Even glory agreed with me that Synths are not human, a bit of memory adjustment, courser uniform, only dreams now.

Unfortunately, that Patriot quest should be the last turn around since the leaders of the contending factions cannot be replaced.