Reproduction steps:
1. Open the attached project "TwoScenesOneMesh"
2. Open the scene "Loader"
3. From the menu select Simple Bundles->Build
4. Play the game
5. Notice in the game window that a mesh was loaded (no material is intended)
6. Exit play mode
7. Add scene "Scene2" to the "bundle" AssetBundle
8. Repeat steps 3 - 4
9. Notice that this time a new GameObject was created in the scene, but it has lost reference to its mesh and is invisible in the game window

Note:
1. References to scripts are also lost