Storing reference to another prefab not working

I am using PrefabUtility.SaveAsPrefabAsset to save a prefab from an AssetPostprocessor. I have another prefab that has an array of GameObjects that reference the other prefabs saved with PrefabUtility.SaveAsPrefabAsset. However, when I look at the saved prefab, all those references say "Missing (Game Object)".

This is the code I'm using:

Code (CSharp):

1. GameObject A;
2. string pathA;
3.  
4. // ... parse files to generate GameObject A
5.  
6. GameObject savedPefabA = PrefabUtility.SaveAsPrefabAsset(A, pathA);
7.  
8. AssetDatabase.SaveAssets();
9.  
10. GameObject B;
11. string pathB;
12.  
13. // Assign references of savedPefabA to GameObject B's component
14.  
15. PrefabUtility.SaveAsPrefabAsset(B, pathB);

This used to work in Unity 2018 with PrefabUtility.ReplacePrefab() but that method is now obsolete.
If I link the prefabs in editor manually it works but I need to automate this in the AssetPostprocessor. What am I doing wrong?

 

Thanks for your reply. I was able to create a small project that reproduces the issue and filed a bug report.