Have you considered to root your phone and uninstall WhatsApp? Is the first time that I see WhatsApp is pre-installed. Even so, you have all the reason, should be an option to restore instantly.
Are you sure that you can't uninstall WhatsApp?
When you have your Google Account configured and you start WhatsApp for the first time it asks you for a restore.
You have to Unlock Bootloader http://forum.xda-developers.com/mi-4c/general/guide-unlocking-mi4c-bl-verification-t3336779
Then install MultiL ROM from xiaomi.eu http://xiaomi.eu/community/threads/6-4-21.31210/
I've already solved . You can try, perhaps work for you.
The problem was the driver. I have deactivated the Windows Update search of the driver and selected the drivers of Qualcomm. These drivers are in: C:\Program Files (x86)\Xiaomi\MiPhone\Qualcomm\Driver (or wherever you install MiFlash)...