According to a report on German website GameStar – appropriately titled “This is not the co-op we want” and allegedly based on info supplied at E3 – only the co-op host’s game progress will be saved, and the other person will have to do everything over in their own game. This is very much like the co-op in Far Cry 4, where completed activities like taking over enemy bases and radio towers and whatever were also only saved in the host’s game. Annoying then too, perhaps, but much less of a problem than, you know, playing the whole campaign again because because.
For the moment, Ubisoft hasn’t confirmed or denied this so maybe it’s a misunderstanding or something, but if it’s true, that’s a real bummer. It’s also a totally inscrutable decision on the developer’s part, given that Wildlands managed to save everybody’s mission progress in co-op. Different engines and different studios, I know, but this shouldn’t even be a thing.