OK, so I’ve run into a very nasty glitch.
I started the civil war on one of my characters and got up to the battle for Whiterun. I went to talk to Legate Cipius, but I ran into this glitch where guards won’t try to arrest me for my bounty and just say “Wait, I know you…” when I press E on them. Since Cipius is technically a guard, he fell victim to this too, rendering me unable to talk to him and thus to progress through the quest.
According to the wiki, this is a known bug, and you can fix it by just attacking a guard. So I hit one of the guards and nothing happened until I killed him, at which point another guard finally tried to arrest me.
So I used my thane get-out-of-jail-free card to eliminate the bounty, but the guard went right back to attacking me. According to the wiki, this is also known, and you can fix it by simply fast-traveling somewhere else and back. This worked, for the guards, but when I went back into Dragonsreach the Jarl, his housecarl, and his steward were all hostile to me. Yielding to them didn’t seem to work and I got killed pretty quickly every time I went inside.
The only save I have before this point is one way back before I even started the civil war quests. I’m going to try to fix it using console commands when I get home, but if that doesn’t work, does anyone know what might? I have no idea what’s causing this.
Edit: Actually I might just be able to fix this by fast-traveling away and back and just making sure that 48 hours have passed.