First the best way to go is to clone the drive.
Then Then use chkdsk /Bchkdsk /B
on the new working drive.
Now as far as unmarking a real bad sector that is tricky. You You could use SpinRite(grc.com) or mhdd (turn remap ON) Either:
- SpinRite, or
mhdd
(turn remap ON)
Either product should remap the bad sector then CHKDSK /B should unmark it.
Download gpartedgparted or partedmagicpartedmagic ISO.
http://gparted.org/download.php
Boot from it, and shrink the partition. This
This will work because windows is NOT running so this software shrink the partition no matter what. Then chkdsk /Bchkdsk /B
will handle the rest.
If all this fails you are now in for an ugly road of pain. You You need to get a sector editor and manually edit the file system. Unfortunately, it is beyond the scope of my knowledge for NTFS. For FAT or FAT32 it is super simple.