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It's impossible for this to be consistent since Project-GC does not override the country selected by the user on Geocaching.com. This means the option is that you can either have Russia/South Federal District/Crimea and Russia/South Federal District/Sevastopol or you can have Ukraine/Kherson Oblast/Crimea and Ukraine/Kherson Oblast/Sevastopol. No matter which one you use you will "lose" the region and county for all the caches marked with the other country. Russia was selected as the country for Crimea and Sevastopol because the only local hider have selected Russia as the country for their caches. If possible I'd say the locals opinion should be given more consideration than the tourists opinions. If you want to have a county and a color on the map for this cache I would consider to politely ask the cache owner to change the country to match that chosen by the locals.