Reshoots of certain scenes might be an option; there were many new scenes shot for Zach Snyder's Justice League with several of the stars, so its not unheard of to go that route.
At this point, no one knows how much of a role (or screen time) the other characters play in the Flash film, or rather, how much time Miller takes up, but Keaton's inclusion--and his appearing in the Batgirl movie--could lead to using him not just as the bridge to that alternate reality, but more of the focus for this film (in subtle ways), allowing the set-up for that next phase, where the Flash would undoubtedly be re-cast.