I still think it would be extremely unlikely, if not impossible, for the Sphere Builders to return (if they survived, which is not entirely clear) and get the Expanse back up at all, let alone to cover 1/4 of the galaxy as shown in "Azati Prime". As has been pointed out, that would take too long. Even if the Sphere Builders immediately started over after "Zero Hour" destroyed the Expanse, there's no way they'd have enough time to cover a quarter of the galaxy in only 400 years. And like I said, they wouldn't consider it worth the effort, either. Now that it's common knowledge how to destroy the Spheres themselves.
Let us just accept that the 26th century as "Azati Prime" showed was an alternate timeline, nothing more. Wouldn't be the first time, either. Daniels showed it to Archer to manipulate him, because that's the motivation behind everything Daniels ever said to him.