I'm making more progress, and hope I can release the modcomp soon.
I'm having problems, though, with the graphical representations of cities. I'm removing and destroying the entity like before, but for some reason cities that are in your visibility when you switch maps remain on the map. Of course the map itself changes, so the cities end up as often as not in the water somewhere. The city itself is not there--if you try and enter the city screen nothing happens, but it still appears as if it's there. One thing I thought was interesting is that when you click the city bar of the city that isn't there nothing happens, but when you switch back to the map with the city, that city is selected.
This only happens with cities that are in your visibility range when you switch maps (though the city bar appears for all the cities in worldbuilder, for whatever reason). I can stop the problem by removing visibility from the plots before I switch the maps, but this messes up the visibility once I switch back.
Any ideas on how to fix this?