I finally upgraded Windows 8 to 8.1 on my laptop today. Yes, I know Windows 10 is available and I am behind time.
The installation (took almost four hours!) was completed with only one problem: it rendered my boot-loader "rEFInd" temporarily unusable. No panic. Nothing happened to the refind directory and nothing was deleted. The following steps will get refind up and running again: (I just copied and pasted part of the instructions from rEFInd's author Roderick Smith's website)
1. mountvol S: /S in the Administrator Command Prompt window
2. cd EFI\refind
3. bcdedit /set {bootmgr} path \EFI\refind\refind_x64.efi
That's all. Basically I just needed to reset rEFInd as the default EFI boot program.