To reproduce:
1. Open the attached project (repro.zip);
2. Reimport "BELT_leather" sprite (Assets > Sprites > Test1 > bow);
-"SpriteSheets" folder will be created;
3. Delete "SpriteSheets" folder (Assets > SpriteSheets);
-notice it is still shown in the Project Window.
4. Restart the project;
-notice "SpriteSheets" is gone.
5. Reimport "BELT_leather" sprite (Assets > Sprites > Test1 > bow);
6. In the "SpriteImporter.cs" comment out 122 and 135 lines;
7. Delete "SpriteSheets" folder.

Expected result: deleted folder does not stay in the Project Window after calling AssetDatabase.StartAssetEditing().
Actual result: deleted folder stays in the Project Window after calling AssetDatabase.StartAssetEditing().

Reproduced on versions: 2017.1.0a6, 2017.1.1p3, 2017.2.0f2, 2017.3.0b3.