For me I've been upgrading the ones I absolutely do not want to ever farm FATEs on, as strictly only zenith weapons are able to acquire atma (why it is this way, I'll never know)

Technically, after upgrading a zenith to atma, you can get your zenith back by visiting the Calamity Salvager and coughing up like 27k gil (and another 900 myth tomes), but who the hell wants to do something like that?