The answer to your question is not a simple one, since there are many things that could cause a villager to "go missing" during the course of a game. If you're running v1.0 of the game (unlikely, since you started playing it recently), there is a bug that causes villagers to actually disappear.

Apart from that bug, villagers can seem to vanish from the game for a variety of reasons. How old was Keopi? It would be helpful to know that, so that I may give the most plausible explanation!