If we're going by Bat-Keaton's explanation of time manipulation, then Barry's actions, however small, impact the past and present. While Barry left the 1989 Batman to perish during Zod's attack, it doesn't mean he's dead. Well, no, that Bat is clipped for sure. However, by going back in time and ensuring his mother dies, he then creates another timeline that never saw Barry go to Wayne Manor for help. This means that potentially he never leads Keaton's Batman back into action. Like the old man said: "Maybe in another time."
By that logic, he's not the only Batman that's safe from harm. Given where Barry initially went back through time in the film's first act, Ben Affleck's hulking hero (with a now questionable-looking cowl) is still probably waiting on The Flash to check back in with him. Just because Clooney is now the new variation doesn't mean it's erased the previous one from existence. He's no doubt hammering tires and pulling chains in the Batcave, hoping not to see Barry return as a floating head telling him that, for some reason, Lois is the key. Simpler times, eh?
