If the app is open while the phone goes to sleep, on returning to the app the VR view is completely squashed and cannot recover.
Swapping between cardboard & 2d VR devices doesn't fix the issue.
Reloading the scene doesn't fix the issue.
The only way to fix is to close and reopen the app entirely.

Steps to replicate:
1) Run the app.
2) Put phone to sleep
3) Wait for the phone to sleep
4) Wake phone up

Result: VR view is squashed

Reproduced with: 2017.2.0b3, 2017.1.0f3, 5.6.2p3.
Not reproduced with: 5.5 (no VR support feature in Player settings).

Tested with: iPod 6th gen iOS10.2.1, Xcode 9.0 beta3.

Note: builds running on 5.6.2p3 don't exhibit this issue 100% of the time, however, it can still be observed if you leave the phone on sleep long enough.