NTFS; marking sectors bad using Linux

To mark sectors as bad on an NTFS filesystem requires modification and knowledge of the hidden "$BadClus" file. I'm not sure of a Linux utility capable of editing that file.

I was under the impression that a non-quick NTFS format would scan the hard drive and mark bad sectors to skip later. Have you tried just reformatting the drive with bad sectors in a Windows VM using either the FORMAT command or diskmgmt.msc and then do a chkdsk to see if it reports the number of bad sectors consistent with what you've discovered?

man mkfs.ntfs sais:

 Basic options
       -f, --fast, -Q, --quick
              Perform quick (fast) format. This will skip both zeroing of the volume and bad sector checking.

I suppose that if the flag is not used, a bad sector checking would be done