Steps:
1. Open attached project and load SampleScene
2. Select GameObject prefab instance in the scene
==>
It has 'FloatVariable' value overriden to 5
3. Open 'TestScript' in Code Editor
4. Comment out the FloatVariable field
5. Back to Unity
==>
'FloatVariable' disappears from GameObject instance
6. Back to Code Editor and uncomment 'FloatVariable'
7. Back to Unity
==>
'FloatVariable' has default value that is 0

Workaround: Reload scene will reapply overrides back to the prefab instance
Please, take a look into attached movie for details