I tried coop today with my brother when he quit and I quit the game it asked me if I wanted to save my progress, I'm guessing you didn't save? (I played on pc btw)
I have a save that says 61% done.. when I load it.. its the first mission. I played the whole game with him so not sure what the deal is. I have been saving every 30 min or so the whole time we have been playing. And the mission that I lost out on I guess I am just SOL even though I was there and helping.. it never registered that I did it.