How to reproduce:
1. Open the attached project ("case_1139245-Bug-PrefabReference.zip")
2. Open the repro scene ("repro")
3. Select the "Test" object in the Hierarchy and add "Zipbot-Legs" prefab reference to it
4. Select "New Scriptable Object Reference" in the Assets folder and set "Zipbot-Legs" prefab reference to it
5. Reimport "Zipbot-Legs" asset
6. Inspect the set references on the "Test" object and the scriptable object

Expected results: References remain unchanged
Actual results: References are missing

Reproducible with: 2018.3.10f1, 2019.1.0b9, 2019.2.0a9
Couldn't test with 2017.4 and 2018.3.0a1 - 2018.3.11a1 because reproduction requires improved prefabs

Fixed in: 2018.3.12f1, 2019.1.0b10, 2019.2.0a10