Hmm? I know it puts the absolute path of the CMake that generated the cache file in there, but what else cares about the CMake version that shouldn't also be reconfigured when CMake changes anyways?

FWIW, CMake is highly relocatable and doesn't really care where it ends up living. That Homebrew removes versions you were using out from under you is not something we can fix. Or maybe I'm not understanding the problem fully (I don't use Homebrew with any consistency to know what the issue is here).