How to reproduce:
1. Open the attached “IN-133920” project
2. Open the Scene “SampleScene”
3. Enter Play mode
4. Observe the Console window
5. Exit Play mode
6. At the top of the window press Reproduction → Assign EntityPrefabReference
7. Enter Play mode again
8. Observe the Console window and the “My SO” ScriptableObject

Actual result: From the DebugLog, you can see that EntityPrefabReference field in the ScriptableObject is filled, but in the inspector it shows "None (Game Object)"
Expected result: Inspector correctly reflects changes made to the ScriptableObject through code

Reproducible with: 2023.3.0b10, 6000.0.67f1, 6000.3.8f1, 6000.4.0b8, 6000.5.0a6
Could not test with: 2023.1.0a1 (package errors)

Reproducible on: Windows 11
Not reproducible on: No other environments tested

Note: When you set the variable through dragging, and the set it again through code, field updates and shows “None (Game Object)” again