In S03E08 "Twilight" Archer became infected with the parasites which kept him away from his duties due to long term memory loss. I think it's safe to assume that the Xindi still went back in time to 2004 to build the bioweapon to destroy humanity like in the events of S03E11 "Carpenter Street". If Archer wasn't involved in stopping the Xindi bioweapon, how were they stopped?