With the attached project:
0. Make sure the Library folder is deleted
1. Open the project using Unity 4.5.2p2, open the scene f1 (which was created with 4.5.2f1)
2. Notice the "sky" and "player" game object's sprite renderers have a missing sprites. The "player" prefab also has a missing sprite.
4. Compare the player.prefab file with the player_p2.prefab file. Notice the sprite fileID in player.prefab references fileID: 21300000. The prefab creted with 4.5.2p2 references the fileID: 21300002, thus causing the missing sprite.

General steps to reproduce (without attached project)
1. Create a 2D project with Unity 4.3 to 4.5.2f1.
2. Add a sprite to your project (notice the sprite meta file will contain the fileIDToRecycleName: 21300000
3. Add a sprite to the scene.
4. Create a prefab out of the sprite added (notice the SpriteRenderer component of the prefab references fileID: 21300000, as expected), and add it to the scene
5. Save the scene.
6. Now delete the library folder and open the project with 4.5.2p2.
7. The sprite you added with now be missing.
8. If you create a new prefab with the sprite in 4.5.2p2, the SpriteRenderer component will now reference fileID: 21300002, even though the sprites meta info still shows 21300000
9. This happens with every sprite in the project, so for large projects, it makes upgrading impossible.