Steps to reproduce:
1. Open the attached user's project "BugRepro_PhantomReferences.zip"
2. Right-click on any of the scriptable objects and use the custom method "List References" to see the list of references returned through
AssetDatabase.GetDependencies
3. See that the two scriptable object correctly reference each other (as well as their script)
4. Edit the scriptable script to remove the reference field named "referenceFieldtoDelete"
5. Use the "List reference" right-click option again to see that the reference is still being picked up.

Expected results: The reference is no longer found
Actual Results: The reference is kept as long as the scriptable doesn't get re-serialized.

Reproducible on: 2020.3.45f1, 2021.3.19f1, 2022.2.8f1, 2023.1.0b5, 2023.2.0a5

Notes:
-Another way to reproduce the same or similar issue is to do the same manipulation on the "TestComponent" that has been added to the "PrefabParent" and "PrefabChild". You'll see that, since the prefab child overrides the reference field value, the reference still gets picked up by "AssetDatabase.GetDependencies" as long as the prefab isn't reserialized.