Spider-Man: Homecoming mentions Peter’s room being across from Vision’s, so Vision hasn’t been missing the entire time since Civil War. The prelude comic acts as if Wanda met up with Vision immediately afterwards, but I don’t really trust those prelude comics.
Honestly we don’t have much to go on. I mean, presumably the rest of the Secret Avengers aren’t only staying in Edinburgh. They’re all close enough to come running when Wanda calls in the middle of a battle, so she must have been sticking with them.
So my gut leans towards Vision and Wanda meeting up on more clandestine interludes rather than being with Vision the whole time.
Those Celestial Bodies 