Hasn't Pax been busy setting up Dissonance pools and using Ex Pacis for some nefarious purpose? Who knows what Dissonance is capable of, after all; Deus touched by Dissonance is a frightening possibility if you ask me.
What I am wondering after reading the short story in Lockdown where we actually see the flash point play out is if she actually intended for things to play out this way. It was Cerberus who (desperately) told the researcher to do something or other to increase his control. I got the impression that without the hapless scientist's timely intervention Deus would have overwhelmed Cerberus and totally overwritten Eliohan's brain, so I've been running my lockdown campaign with the assumption that this had been Pax's original plan - Deus's personality contained in a single body, even if it is a dragon, would be theoretically easier to predict, counter, or control. Obviously a returning Deus would draw a lot of fire from, like, everyone. Maybe that was her plan - use a powerful but manageable re-creation of Deus to distract everyone from her cooking up dissonance wells all over the city. Plus, she get the satisfaction of seeing Deus killed a second time.
In my campaign, Pax is kind of running scared. She's not sure exactly what she's wrought here, or if she is going to be able to manage it. I don't think this is what the devs intended, based on their comments here, but my own interpretation is that she did salvage portions of code from the genuine Deus, so that it IS Deus in that sense, but she was able to do a pretty basic patch up on it, and it's a shadow of what it once was. I'm stating it up to be a standard, albeit powerful standard AI with attributes and everything that make it, in theory, possible to defeat through conventional matrix combat - at least once it finds a way to get itself out of people's brains and into devices. Once that happens, though, it's going to have its eye on those old ECSE servers as a means of upgrading itself, as suggested in the Lockdown book's discussion of the Harbor Guide system