I think I managed to solve the issue. Pretty simple once I found the right process. I used CASPER V7 for that (www.fssdev.com
). I created the bootable recovery media (WinPE 3.1 based apparently), I cloned the OS partition in standard mode (= file by file copy) to a partition located an external USB HDD disk. Took 2 hours. After that, I cloned back the OS partition (external drive to internal drive), using AccuClone mode (= sector mode), took just 12 mins.
After reboot, and chkdsk at boottime, the major NTFS corruption was gone.
The "trick" was to use file mode for the first cloning, because using sector mode only transported the issue.
Thanks to all who made suggestions. I now get as a bonus, among various things, the link to MSFT & Sophos antirootkit, and the very useful Fake Name Generator URL.