Odd thought that popped into my head while contemplating a late dinner (don't ask me why, my brain is a rat maze).
But I had a thought about where the AIs went. They went into the people.
We have evidences of phenomenal levels of technology. Including nanotechnology that can perform something not dissimilar to magic.
We know the functions of the praesses were hijacked by something that allowed Ardent and Gavina to become embodied and travel to earth. From a basic data intrusion standpoint, that's easier to do if you already have network access rather than trying to force your way in from the outside.
We also know that the Praesses create virtual worlds from scratch, an "inner reality" that they populate with, for want of a better word, digital copies of humans. Their goal of making it effectively no less "real" than the outer reality suggests that these digital copies would be complete down to the finest detail.
So suppose the AIs, knowing that continued warfare would only push both sides closer to complete extinction, wrote themselves into the human genome and exist as just another part of human microbiota, borrowing from the body for whatever they need to function alongside all the other bugs that hang around on and inside us, maybe writing to our unused (junk) DNA for storage space, drawing excess thermal or bioelectric energy to power any major actions, communicating with each other through human interaction or physical contact. Maybe even influencing people to a degree by tampering with brain chemistry to facilitate communication between each other, and maybe to keep the peace. Humans lost their ambition, as Pate described it. Maybe that was intentional, in order to prevent another cataclysmic war.
So the praesses. They're alien, they'd have no frame of reference of what a human's genome and microbial hangers on are supposed to look like until they get a look at one. So they make their virtual humans, and inadvertently replicate the AIs along with them. These spaceborn AIs figure out where they are, what they are, and how they are, and they see an opportunity to fix everything. Since they're already running on the Praesses network, they gradually figure out how to subvert it to send their chosen agents to earth.
Apologies if someone's already suggested this.