My personal theory is that the Human Sunset Shimmer ran away from home the same time the Pony Sunset Shimmer did. She probably went off to New York City or Hollywood to seek her fortune.

However, lets keep in mind that the humans with Equestrian counterparts were a tiny minority at the school. Just because a familiar face (such as Lyra, Bonbon or Octavia) isn’t there is no reason to think that they’re dead! They might just live somewhere else.