I ended up getting this working by using this post.
I added it to AstarData.cs and had to change
var sr = new Pathfinding.Serialization.AstarSerializer(this, settings);
to
var sr = new Pathfinding.Serialization.AstarSerializer(this, settings, active.gameObject);
I also had to downgrade off of the beta version due to it not allowing me to edit the scripts. But its working now. When my tiles spawn/despawn their graphs go with them.