It does cause WW, because it counts as 'losing' a city to enemy action. In my current personal game I am so fed up with flips that I am rushing settlers, putting them in recently captured cities and abandoning them and building my own city in the same spot, generally. So Odense becomes Was Odense. I'm going for a Domination victory. I am keeping Wonder cities and just dealing with flips there. Anyway, the flips are part of my level 2 WW. My only productive cities are my core, anyway, and they aren't as bad due to various factors. Strangely enough, my Specialist farms are going nuts, but it doesn't affect their science output. I'm still getting decent research times with 50 cities in disorder. It does make the IBT a PITA with 50 disorder reports. Hopefully I will win soon.