SerializedObject data wipe when applying to prefab

Like so many others I am having terrific frustrations trying to get a custom editor to set data on my objects/prefabs and have it save. After following the guide on this thread, my code looks like this:

First, the storage container class and the actual custom component:

 [System.Serializable()]
 public class CreatureAnimationPair : Object
 {
     public string animationHandle { get; set; }
     public CreaturerAnimationType type { get; set; }
 
     public CreatureAnimationPair (string animationHandle, CreatureAnimationType type)
     {
         this.animationHandle = animationHandle;
         this.type = type;
     }
 }
 
 [System.Serializable()]
 public class CreatureAnimation : MonoBehaviour
 {
     public List<CreatureAnimationPair> animationPairs;
     
     ...
     
 }

Then, the editor class:

 [CustomEditor(typeof(CreatureAnimation))]
 public class CreatureAnimationEditor : Editor
 {
     SerializedObject creatureAnimationSO;
     CreatureAnimation creatureAnimation;
 
 void OnEnable ()
 {
     creatureAnimationSO = new SerializedObject(target);
     creatureAnimation = (CreatureAnimation)target;
     
     Animation animation = creatureAnimation.gameObject.GetComponentInChildren<Animation>();
     if (animation != null && creatureAnimation.animationPairs.Count <= 0)
     {
         List<CreatureAnimationPair> newPairs = new List<CreatureAnimationPair>();
         foreach (AnimationState anim in animation)
         {
             newPairs.Add(new CreatureAnimationPair(anim.name, CreatureAnimationType.None));
         }
     
     creatureAnimation.animationPairs = newPairs;
     
     EditorUtility.SetDirty(target);
     EditorUtility.SetDirty(creatureAnimation);
     creatureAnimationSO.ApplyModifiedProperties();
 }

In this case, CreatureAnimationPair is an enum set I've made. When I use this on a creature instantiated in the scene, it'll go through all its animations like I want it to and fill out the list of pairs. I can see them in the inspector using my custom GUI just fine. But as soon as I apply that to a prefab version of the creature, all the data in that list gets wiped -- all the strings are emptied and all the enum values become garbage. Why is this happening? How do I get the changes I make in the scene to persist into the prefab?