Repro steps:
1)Open the later-attached TestProject
2)Notice TestPrefab.prefab, it's otherPrefab field and open it in text editor
3)In the text(YAML) file notice two mentions of the otherPrefab: in the MonoBehaviour section and in the Prefab->m_Modifications
4*)Open TestPrefabScript.cs and comment line 6 (the only proper line of code)
5) Save the script, make a change to TestPrefab, and save the scene
6) Open up the TestPrefab.prefab in a text editor again
7) Notice there is still a reference to the otherPrefab in it

Reproduced in: 5.4.0b10; 5.3.3p3; 5.2.4f1

Expected behavior: unused field is cleared from the prefab data and doesn't get involved in AssetBundles