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ChkDsk on Startup, deleted "corrupt" files; Programs no longer work.
So earlier today, Windows told me it had an update to install. So, I shut down my computer like normal, then booted it back up. In the middle of booting, the black Check-disk screen came up (which is unusual), said something about the C:/ drive being NTFS and needing to scan it.
It then proceeded to delete numerous "corrupt/orphan" files, which was even more unusual. Sensing something wasn't right, I hit my reset button to stop it from deleting anymore files, and avoided the check-disk scan during the following bootup.
My instincts appear to have been correct, as numerous programs can no longer function. Firefox fails to start because its "side-by-side configuration is incorrect." Ifranview appears to have had its core program deleted, but left shortcuts. iTunes "was not installed correctly." Those are just a few examples, but there are more programs such as Adobe that appear to have had crucial files deleted/corrupted. Luckily Internet Explorer *shudder*, my pics/docs/vids/music, and a few other programs appear to be working for now. I tried reinstalling Firefox, but that appears to have done nothing.
I already plan on moving/backing up all of my pics/docs/vids/music and project files to an external hard drive before doing anything else, and I've run Avast! and Malwarebytes scans but found nothing...
So here's my question(s): What the heck happened? What caused this, and is there a way to fix it without wiping my entire hard drive, reinstalling Windows 7 and starting over from square one?