Best bet would be to get the files and reformat. Basically the same thing happened to me, but I decided to do a hard reboot.

oops is all I can say >.>

Now I run with a backup image of my os and files on a separate disk. my current disk is a raid 10 in hopes that a HD failure does not screw me again.

not sure what exactly happened to cause the complete redoing of the file system. typically chkdsk doesn't screw that badly with your system unless something happend.