Upgrading to Windows 8.1

Hi,

I am sort of worried; I installed windows 8 without a problem, and then i decided to upgrade to windows 8.1, frist I upgraded the drivers to BootCamp v5.1, I initiallized the upgrade and everything went without a hiccup, however, it restarded and started ''Analyzing and repairing Disk (G:)'' I know I should be patient, but it's taking too long and I'm worried that this ''repair'' might end up messing with the bootloader or something like that. Is that message normal? Do I continue on waiting? If it isn't normal, what should I do?

Thanks, in advance.