In order to Refresh a Windows 8 to 8.1 system, you need the 8.1 install files or a Custom Refresh Image you may have created. If you don't have either, then a Refresh is not an option.
To Reset your system, you would need to use the OEM reset or Windows 8.1 reset options to put your system back to Windows 8 as it was from the factory. If you have the image on a Recovery partition on your hard drive, it would be able to accomplish this procedure, but it depends on how your system is configured.
Calling the OEM and obtaining the necessary media may be your best bet if the Reset option is not usable for whatever reason.
As far as the error message, the file is used during the booting process. Perhaps it was corrupted by the malware...