The issue only occurs when the scene view is closed. If the scene view and game view are open side by side, everything works fine.

To reproduce:

1. Open the project, attached by user (TEST1.zip)
2. Enter Play mode.
3. Observe the model's head
4. (Optional) When the model fully comes back to view and head has disappeared, pause the gameplay and increase the Main Camera's z position

Expected: parts of the model should not become separated when the model with an animation comes back to camera view
Actual: head of the model separates from the body when the model is clipped by camera and comes back as soon as the camera is moved or the scene view is opened

Reproduced in 5.5.4f1, 5.6.1f1, 2017.1.0b9, 2017.2.0a3