The sphere builders didn't see themselves losing with certainty; they can't - they didn't see Archer destroying the spheres (the future isn't fixed in star trek). They saw the future of them losing is probable AKA NOT certain.
As for the spheres destroyed in S3 being integral their plans - in Enterprise we saw them transform space with blinding speed.
They tried it again, with a new round of spheres/their technological successor in the 26th century, this time transforming space at full speed. This time, they were stopped at Procyon 5.
Which is the only version which fits what Daniels said and the scenarists' intent (as displayed in the relevant sequences, etc).
Any other interpretation leaves you either willfully ignoring large parts of the sequences, their tone, etc ('momentous event in history', etc) or with FAR larger inconsistencies (the federation not existing to fight if Archer failed; Daniels not caring about massive alterations to the 26th century, etc).
The entire point of the TCW was to make changes in the timeline and excuse the retcons made in the show.
Daniels says to Archer that history had changed first with the destruction of the colony on Paraagan II ("Shockwave") then again, and most important to this discussion, the Xindi attack on Earth from "The Expanse". That's explicitly said to be a huge change. He later shows Archer the battle in the future that led to the Builders making that change. The Battle of Procyon V will no more happen in the future of ENT/TOS/TNG/DS9/VOY than Kirk will land a Bird of Prey on (nonexistant) Vulcan in the future of the STXI timeline.
The Sphere Builders were able to accelerate their transformation of space only after the Spheres had been doing their work for thousands of years. They won't be able to recreate the Expanse in the 400 they have. If they could, they'd have done so immediately after placing the spheres, long before their rivals achieved spaceflight.