So, I got the missions: Either kill Desdemona or warn her to continue the Railroad story line. If I talk to her she doesn't react, only says the standard sentences like "I'm busy".

I've googled a lot about it, Glory is alive and in the Railroad HQ, Deacon is somewhere but I can't even find him even with console commands. This gamebreaking bug exists since the release and is not fixed by any of the patches. I have installed the newest 1.3.45.00 Beta-Patch.

But anyway, is there a solution that I've overseen?

Did you do all their quest?

reload an older save or restart the game

Sounds like you accepted a quest and haven't completed it...or you have taken a quest for another faction that overwrites the RR quest, meaning that you can't finish the RR quest.

Shoot PAM in the face, it will solve the RR quest issue

I have 2 quests left: Kill Desdemona or warn Desdemona!

I have completed ALL the Quests for the Railroad (at least I don't get new right now). I built all of the MILA's and killed dozens of runners. For the Institut I made 1 single sidequest. That's it.

As soon as the Synth talked to me and the Railroad Quest whent to "warn Desdemona" I tried it. Didn't work. So I whent back to the Institut where I had the quest "talk to father". He only told me to kill Desdemona, thats it.

I just don't get where the mistake can be. I only did quests for the Railroad, 1 "killing Ghuls" sidequest for Dr. Li and the first mission for the BoS, securing Fort Strong. That's all. I'm not even a Minuteman! So there was not a single quest that effected more than 1 faction, except the quests I did for the Railroad.

Difficult to answer this without dropping multiple spoilers, but if you are given the option to "Kill Desdemona" I think you are too far into the Institute. I'm still part of the RR, but "playing" the Institute, and just chose to warn the RR about something. (You can choose to warn various factions.)

I have not been issued a kill Desdemona by Father, so somehow it seems like you have made a final faction choice - at least your path is reflecting that.

You may have to go back several saves.

I know what you mean, but it can't be. The only faction choise I made was to make the BoS enemies doing the Mass Fusiun quest given by the Institute. But you have to do this for the Institute because the quest for the Railroad tells you to continue to work for father. And as soon as I had finished working for father I went back to the RR without success.

Bugs like this are rampant in the game. I had a similar one where I couldn't finish the Silver Shroud quest line because Hancock was locked into dialogue from a mission i already completed. Only way around it was advancing the quest to it's end via console commands. It svcks for those who play on console, and it also svcks because you need to know the proper ID for the quest in question in order to use the command to begin with.

I don't think it's a bug.

@OP:

When you spoke with 'Father' and he gave you the quest to destroy the Railroad, you had an option of either saying the Railroad is your ally, in which case you get the two options of either killing Des, or warning her; If you say that the Railroad is not your ally, then you only get the option to kill Des...otherwise, she brushes you off, and everyone else ignores you.

Sounds like you made a conversation choice with consequences, and are stuck with it.

Advice is to either carry it through, as you've made your ally choice, or go back and reload an old save, from before you spoke with 'Father' and he gave you the quest.