That option may necessitate you returning your machine to Factory Settings that you had at "Day One".
Most new machines come with a recovery partition allowing you to go back to the time of purchase, you will have to check your user guides (or the manufacturer's Web Site) for instructions. Choosing that path requires you to save all valuable data first. Unfortunately upgrading to Windows 8.1 may lose such Recovery Partition.
Windows 8.1 Update Leaves OEM Owners With Broken Restore Function
Warning! If You Upgrade to Windows 8.1 Through Windows Store, You May Loose The Ability to Refresh and Reset
This (following) might need to be done if you want to fix the problem on your own machine as I believe that all of the above recovery options will fail because of your current fault of "missing files".
This is what you might need to do. It might reinstall the missing files.
Try contacting your OEM for the Windows 8 Recovery Media. For a small charge they should be able to supply you with a copy on DVD or USB. This will allow you to reinstall Windows 8 to factory settings as of day one.
The above would be the same procedure as if you had corrupted, lost, or replaced, a faulty hard drive, which often happens.
Perhaps this is a workaround too?
Create installation media for Windows 8.1
http://windows.microsoft.com/en-us/windows-8/create-reset-refresh-media?ocid=tp_css_createmedia