Sov de levelling problem

In one of my cities I ran out of research points and all my sov was rescinded. My sov is still showing on the map and in the city sov view, but I get no bonuses from it and no upkeep is needed. I can't do anything with that sov spots. I tried to start claiming sov again, but I can't since it says "maximum sov level has been reached" I can't delevel it either. So I'm stuck with non functional sov spots around my city. 

Problem is that I'm now running -10K food per hour and I can't do anything about it except that I could raze my city buildings to lower the population, but I don't want to do that. With my old sov I was positive in food and barely negative in research points.

I also have a question, why all sov was totally rescinded? I was running something like -20 research points per hour and in some moon cycles I was positive. One level on one of my sov claims de levelled would be enough to get my RP back to positive. Something is seriously wrong in sov de-levelling algorithm. 

P.S.

Can you please also look at my old petition #7759. I can't build any building on empty spot in one of my towns...