Here's a "cheat" that will probably work. As Ladycfii suggests, exit and reload fairly regularly. Now if something bad happens when you're in the game, hit the soft reset button on the back of your handheld. This will cause you to lose everything that's happened since your last save but also loses the lost villagers. I admit to using this when the random events are particularly bad. It's taken me three tries to get a village that didn't fail and I'm not going to allow some stupid random event to totally ruin it! Gah!