Actaully come to find out, the unity navmesh system doesn't allow loading a navmesh from another scene using LoadLevelAdditive. So although this works well for Vuforia's purposes, I can't use it for my original problem. Oh well, thanks for the help though.

I was using the scene name as the key to that hashmap, so I changed it to the name of the image file for the trackable like it's supposed to be. Now it works perfectly!

I don't set anything to keep alive.  It's load level additive, so it merges one of your scenes with the main one that has the ar camera and targets and then destroys it when tracking is lost.  You'll obvisouly have to fill out the trackables hashtable with your own values and make sure you have your scenes added to the build.

Thanks so much for your script! I'm trying to use it now but I don't see my scene information being loaded. I have the ARCamera set to keep alive, but not the ImageTargets. That's right, right? I'll look more into this but this looks like it might be just what I needed! :)

Here's my DefaultTrackableEventHandler that handles multiple scenes with multiple targets.  Your main scene would contain all the targets and the ARCamera.  Each scene would have a root gameobject and no camera.  Async is Pro only i think, so you may have to use regular loadleveladditive.  Also in this script i run an animation script when the level is loaded, you might want to remove those lines.  Hope it helps.

using UnityEngine;
using System.Collections;

public class DefaultTrackableEventHandler : MonoBehaviour,
                                            ITrackableEventHandler
{
	
    private TrackableBehaviour mTrackableBehaviour;
	
	private Hashtable trackables = new Hashtable();

	private static string currentTrackableName = "";
	private static bool loaded = false;
	private static bool working = false;
	public static bool lostQueued = false;
	public static bool isCurrentlyTracking = false;
	
	private const int SCENE_NAME = 0;
	private const int MODEL_NAME = 1;
	private const int IMAGE_TARGET_NAME = 2;
	
    void Start()
    {
		mTrackableBehaviour = GetComponent<TrackableBehaviour>();
        
		if (mTrackableBehaviour) 
        {
            mTrackableBehaviour.RegisterTrackableEventHandler(this);
        }
		
		trackables.Add("", new string[]	{"", "", "" }); //SCENE_NAME, MODEL_NAME (ROOT GAMEOBJECT), IMAGE_TARGET_NAME
		trackables.Add("", new string[]	{"", "", "" });
		trackables.Add("", new string[]	{"", "", "" });
		
		OnTrackingLost();
    }
	
	void Update()
	{
		if (lostQueued)
		{
			OnTrackingLost();
		}	
	}
	
    public void OnTrackableStateChanged(
                                    TrackableBehaviour.Status previousStatus,
                                    TrackableBehaviour.Status newStatus)
    {
        if (newStatus == TrackableBehaviour.Status.DETECTED ||
            newStatus == TrackableBehaviour.Status.TRACKED)
        {
            OnTrackingFound();
			isCurrentlyTracking = true;
        }
        else
        {
            OnTrackingLost();
			isCurrentlyTracking = false;
        }
    }


    private void OnTrackingFound()
    {
		if (working || loaded || lostQueued)
			return;
		
		working = true;
		loaded = true;
		
        Renderer[] rendererComponents = GetComponentsInChildren<Renderer>();
        foreach (Renderer component in rendererComponents) 
		{
            component.enabled = true;
        }

		foreach(DictionaryEntry t in trackables)
		{
			if (mTrackableBehaviour.TrackableName == t.Key.ToString())
			{
				string[] sa = (string[])t.Value;
				currentTrackableName = t.Key.ToString();
				StartCoroutine(LoadLevel(sa[SCENE_NAME], sa));
			}
		}	
    }
	
	
	IEnumerator LoadLevel(string levelName, string[] levelData)
	{
		AsyncOperation async = Application.LoadLevelAdditiveAsync(levelName);
        yield return async;
		LoadLevelData(levelData[MODEL_NAME], levelData[IMAGE_TARGET_NAME]);
		working = false;
	}
	
    private void OnTrackingLost()
    {
		if (working)
		{
			lostQueued = true;
			return;
		}

		lostQueued = false;
		working = true;
	
		if (!gameObject.activeSelf)
			return;
	
		foreach(DictionaryEntry t in trackables)
		{
			if (currentTrackableName == t.Key.ToString())
			{
				string[] sa = (string[])t.Value;
				DestroyLevelData(sa[MODEL_NAME]);
			}
		}
		
		Renderer[] rendererComponents = GetComponentsInChildren<Renderer>();

        foreach (Renderer component in rendererComponents) 
		{
            component.enabled = false;
        }

	    System.GC.Collect(); 
		
		working = false;
		loaded = false;
    }
	
	private void LoadLevelData(string objectName, string parentName)
	{	
		GameObject go = GameObject.Find(objectName);
		
		if (go != null)
		{
			SetParent(go, parentName);
			AnimationScript script = go.GetComponent<AnimationScript>();
			if (script != null) {
				script.begin();
			}
		}
	}
	
	private void SetParent(GameObject child, string parentName)
	{
		GameObject parent = GameObject.Find(parentName + " Plane");
		if (parent != null && child != null)
		{
			child.transform.parent = parent.transform;
			child.transform.position = parent.transform.position;
		}
	}
	
	private void DestroyLevelData(string objectName)
	{
		GameObject go = GameObject.Find(objectName);
		if (go != null)
		{
			AnimationScript script = go.GetComponent<AnimationScript>();
			if (script != null) script.end();
			Destroy(go);
		}
	}	
}