Well, let’s run this one up the flagpole and see if it gets shot off. I posit that detection of noncons is imperfect, and that the system for deploying them is capable of being corrupted.
Why Pablo, I’d never dream of shooting down your flag. And luckily, here there is no need as this is perfectly on-message and just the kind of thing that I’d have written myself if I wasn’t too busy with simultaneous storylines involving the post-mortem computer-modelled consciousness of a newly ascended saint and a mysterious alien on the run from totalitarian Church authorities in a rickety old shuttle (and at present failing to find the time to write either).
I imagined that the detection of noncons is fundamentally flawed in principle even if it is accepted to work in practice, as it assumes that there is some measurable physical correlate of a subjective state. In the case of your story, it seems that it is the post-detection surgical zombification that has gone awry and left some of those inconvenient memories intact.