I've saved and reloaded the game, which seemed to have fixed the problem. I got my population back, and that doppelganger is gone.
However, some time later, I noticed that my capital has changed back to the last province it was in (Kiev) before I moved it to the new one in Wallachia. Also, I got TWO nomad settlement holdings, in both Kiev and that province in Wallachia. The one in Kiev has no upgrades, while the one in Wallachia has all the upgrades I've did previously. So, I essentially lost all my upgrades, since I'm guessing that most of the bonuses are calculated from the capital.
Anyway, it's clearly a bug that I'm able to get two nomad settlement holdings.
EDIT: I loaded back an earlier save. It seems that no matter what happens, my ruler will clone himself upon his death.
EDIT: I reloaded again and tried to split clans before my ruler's death so that I have 9/9 clans to see if that made a difference. It didn't, upon my rulers death, I got 10/9 clans and a copy. Same as before.