Well, here is what I heard:
White Forest/Black City, both exclusive to one of the games decay as you take time reaching there. If you finished the game late and headed t here, then you might see the forest population lower than max. Contradictorily, if you fin ished the game soon, the forest population is higher. So, if you leave white forest alone for a long time, its content slowly decay and its dead. If you happen to have a population and want to keep them, you need to keep visiting white forest frequently and talking to the NPCs there, if not, they lose interest and move out. This is one of Nintendo's suckish tricks to force players to play the game daily.
To get the people back, you need t o use Entralink to visit someone's Black City, i dunno the rest of the process, google it...