Microsoft has just updated the following KB Article:
Deployed applications are removed during upgrade to Windows 8.1 General Availability on a Windows RT-based device
Symptoms:
When you upgrade from the Windows 8.1 Preview release to Windows 8.1 General Availability on a Windows RT-based device, any deployed application that you may have had on the device is removed.
Full details at:
http://support.microsoft.com/kb/2905780