Successfully upgraded to Windows 8.1 and have FFXIV installed after backing up the game files.

I backed up the following folders:
C:\Program Files (x86)\SquareEnix\FINAL FANTASY XIV - A Realm Reborn
C:\Users\USERNAME\Documents\my games\FINAL FANTASY XIV - A Realm Reborn
and FFXIVSETUP.exe

Once I had Windows 8.1 installed I ran the FFXIVSETUP.exe it recreated the C:\Program Files (x86)\SquareEnix\FINAL FANTASY XIV - A Realm Reborn folder and a shortcut on my desktop.
I copied over my backup folders to the original location and launched the game. I was able to play without any updates and my user settings were the same(HUD, keybinding, etc...).