Flipping Cities

I noticed that I could flip cities yesterday while playing BI. By taking the general out of Aquinum? the one with all the religious conversion--and just putting him in a pagan territory he can convert the population in just a few turns. It works better than a whole lot of spies and assassins. In fact I used a couple of those too for good effect. I

I was able to make capital cities riot and actually flipped other non-capital cities.

The problem I experienced after I took those cities and changed the religion to Christianity is up to 60% unrest that lasted longer than 10 turns and never went down.

Has anyone experienced this? I am not sure if the unrest is because I'm taking pagan provinces or because I converted them before I took them and that had something to do with it.

???

You can see what is making a city unhappy in the city detail screen. Go there and look.

Right. I can see there is about 60% unrest. But I can't figure out why I have so much of it and for so long.