The way I have it in my headspace right now is that any and all [i]magi[/i] capable soldiers have been transferred to full authority of the church for the last twenty-seven years. Thus the city-states have lost a degree of autonomy and the system has become much more centralized. I imagine they’ve written some sort of theological writ or law that calls it some sort of reform, but its really just totalitarian reorganization.  

As for the prosthetic, I think it will be fine; though there are two forms of magitek -- the kind that allows mundane usage (such as firearms) and the kind that serve as a focus for the magically inclined.