The Zenith were an ancient race existing far FAR prior to the AI War timeline. I don't know exactly how far back, but we'll say millions of years at the least, possibly as many as billions. They are mostly shell-like creatures that look a lot like the armored golem in AI War. Their spacecraft were partly organic, but unlike the Spire their spacecraft were not actually them themselves. The armored golem was built pretty much in their image, though: like we might build a giant bipedal robot in our own image, if you know what I mean.
The timeline of SBR takes place in the fairly distant future from both AI War and TLF -- neither of which are on the same timeline, themselves, either. Right now it's not clear which of those timelines is actually first, as they are in different galaxies. And it's not clear exactly how far into the future the SBR events are, which are in yet another galaxy.
Suffice it to say, the bulk of the Zenith are indeed extinct, except for those that are... well, I won't really say. They're on this planet, anyway.