So, I'm at the part i the main storyline where I can either kill Desdemona or warn her about a BoS attack on the HQ. I want to warn her but it won't let me. She just keeps saying, "I'm busy" or her two other 'busy' lines and I cant talk to her.

I've tried using console commands to finish that particular quest but if i do that no other quest pops up and I can't progress in the storyline.

bump

Did you take out the Brotherhood on the Pridwing before you got to this point in the quest?

I'm pretty sure that happens after the BoS attack the Railroad HQ which is the part that's bugged for me

Yeah it does. So you havnt done that before you got to this point? Because for me I had aldeady taken them out before I had to warn them about the attack. I had to reload to a point before I took the brotherhood out on the pridwing and redo the quests up to that point. I was then able to get past warning her.