Steps to reproduce:

1. Open attached project "795751.zip"
2. In hierarchy, notice scriptable object "FeatureToggle" and its script
3. Select "FeatureToggle" and notice that it references sprite
4. Open Scriptable object's script and comment out Sprite declaration, save script and return to editor
5. Select "FeatureToggle" scriptable object and notice that there's no Sprite field anymore
6. Right-click on scriptable object and select "Show in explorer"
7. Open asset file with text editor and notice that reference to sprite still exists

Additional steps:
8. In editor's top menu, click "SUPPORT > Build Bundles". Bundle will be built to "[ProjectRoot]/Bundles" folder
9. Open bundles location and open Bundles.manifest
10. Notice dependency between Sprite and Scriptable object bundles

Expected result: Reference is removed after scriptable object's script is edited
Actual result: Scriptable object needs to be marked as dirty manually for references to be updated

Workaround: After editing scriptable object's script, mark it dirty and save assets:
UnityEditor.EditorUtility.SetDirty(scriptObj);
AssetDatabase.SaveAssets();

Reproduced with: 5.1.4f1, 5.2.4f1, 5.3.4p6, 5.4.0b18