//Some serializers allow single entities to be saved, i.e. the YML serializer
//But first, we need to create an entitiy.
RemoteEntity entity = this.npcManager.createEntity(RemoteEntityType.Zombie, Bukkit.getWorld("world").getSpawnLocation());
//Now we can just call the save method. Keep in mind that it will not work when the serializer doesn't support single entity serialization
entity.save();
//To load the entities we saved, you can just do this:
this.npcManager.loadEntities();
//Now all the entities should be back like you never removed them
}