When installing Windows 8.1, the option to keep “Windows settings, personal files and apps” requires that the Windows 8 system matches the system default UI language. In addition, The Windows 8 edition can only be upgraded to an equivalent or higher Windows 8.1 edition.
If the option to keep “Windows settings, personal files, and apps” does not appear on the “Choose what to keep” page in Windows setup, please check to make sure that that you are installing the same language, and that you are using the ISO and product key that matches your currently installed Windows 8 edition.
These are a few of the issues we have seen occur for our customers during the upgrade to Windows 8.1.
Contact Cyrious Support to have your files/folders structure repaired.