Reproduction steps:
1. Open user's attached project "MagicaClothBugReport2019_3" and scene "SubAssetBug"
2. Open "TestObject" in Prefab Mode and make sure Auto Same is enabled
3. Select "DataA" and press "Create Scriptable Object Data" in the Inspector
4. Exit Prefab Mode and open it back again
5. Select "DataB" and press "Create Scriptable Object Data" in the Inspector

Expected result: Both "DataA" and "DataB" Scriptable Object references are not lost
Actual result: "DataA" Scriptable Object reference is lost

Reproducible with: 2019.3.0a1, 2019.3.0f6, 2020.1.0a14
Not reproducible with: 2018.4.17f1, 2019.2.20f1, 2020.1.0a15, 2020.1.0a22
Could not test with: 2017.4.36f1 (errors)

Note: "DataA" Scriptable Object can still be seen as selected in the Inspector after step 5. It changes to None after exiting Prefab Mode or double-clicking on it