How to reproduce:
1. Open the attached 'PrefabDontSaveInEditorBug.zip' project
2. Go to the Project tab -> "Scenes" and open "SampleScene" scene
3. Go to the Hierarchy tab, select 'PrefabCreator' object and click on the 'Create' button in the Inspector tab
4. Expand 'ParentPrefab' and observe 'Prefab' object. Notice the "DontSaveInEditor" checkbox is marked
5. Go to Project tab -> "Prefabs" folder and double-click on "Prefab" asset
6. Modify prefab (ex. change transform position) and make sure 'Auto-Save' is on
7. Come back to the "SampleScene" scene "Prefab" instance and observe "DontSaveInEditor" checkbox

Expected result: Checkbox is marked
Actual result: Checkbox is unmarked

Reproducible: 2018.3.13f1, 2019.1.0f2, 2019.2.0a12, 2018.2.21f1 (a122f5dc316d)