I don't have any evidence whatsoever, so this was almost a comment:
I've seen BvS a couple times, including the extended version. I don't believe there's ever any explanation of what happened to Wayne Manor.
I felt like this movie drew on our collective understanding of who Bruce Wayne/Batman is, rather than trying to re-invent the wheel and waste a lot of time on his background. The most recent, mainstream version of Batman was presented in the recent trilogy starring Christian Bale, starting with Batman Begins.
Clearly, not everything in that series has happened in the past of this new movie, but I think it loosely inspired the new one. Sort of like Hulk and The Incredible Hulk. The second movie there sort of drew on the first one, but ignored a lot of the stupid stuff people hated, like the ending.
I think most people agree that Batman Begins and The Dark Knight were great. I certainly do not agree that the Dark Knight Rises was anything other than a train wreck, much like the ending of Hulk.
Wayne Manor burns down in Batman Begins. It's not rebuilt until Dark Knight Rises.
This Batman never rebuilt it.