How to reproduce:
1. Download and open user's attached repro project "ABTest.zip"
2. In the project open a scene called "Main", then Click "Builder->Build" to build AssetBundle
3. Play "Main" Scene, you will see 3 icons loaded int the Scene window
4. Quit Playmode and change the assetBundleName of the Sprite named "spr_02" from "b.unity3d" to "c.unity3d"
5. Click "Builder->Build" to rebuild AssetBundle and then press Play again, you will find one icon missing

Expected result: Prefab's AssetBundle dependency updates and the Prefab does not disappear from Scene view
Actual result: Prefab's AssetBundle dependency fails to update resulting in that one icon in the Scene view is missing

Reproducible with: 2017.4.11f1, 2018.1.9f2, 2018.2.8f1, 2018.3.0b1

Note: A prefab in AssetBundle named "a.unity3d" depend on 3 Sprites packed in 2 AssetBundles named "b.unity3d" and "c.unity3d". If you delete "a.unity3d" and "a.unity3d.manifest" and then rebuild, problem becomes solved.