I think it was just a booby trap that the AIs neglected to edit out either by mistake or because they though it best if Earth was left without any advanced technology for a period of time.
It also functioned as a plot device that made it possible for everyone to get into orbit. If Gavia still had her nanotech when Pate and Church arrived at the archaeophile site I imagine the latter would quickly overpower Alice and Sedna. However, Gavia would take Pate hostage using a phase shifting dagger as she does later. Of course this would put them at an impasse since Gavia could never let Pate out of her sight, but would never want to bring them with her back to the Praeses.
It's interesting to think what might happen next and I hope we can call come up with some good ideas.
Here's one I thought of that was partially inspired by this strip that Jeph shared on Tumblr and may or may not be able to link to it:
https://68.media.tumblr.com/5416bfd9f458626519e5106f4247471f/tumblr_inline_ot1dm3nT2w1qkjo9f_540.jpgIf Questionable Content is one of the many simulated worlds within the Praeses then perhaps they would share some inspiration as a gift for Gavia who doesn't know what she's going to do with her life now that she'll be living on Earth permanently. It comes to her in a dream. Open a coffee shop! And what we get is a slice of webcomic in the distant future. Gavia would be the Dora in this story and she soon assembles a staff of townspeople to work there. Sedna could be the Faye doppleganger and there'd be a ditzy smart girl who would be Raven and a Sara who is actually devoured by an allosaurus for real and not in a semi humorous attempt to drop a character of little interest. And eventually there would be the savant daughter of Jesper Pate joining the cast.
So what do you think sirs?