It's the first time I use Kaspersky live CD, It was only a prevention scan,
The Kaspersky scan found some suspicious file but they were not infections being ran by my OS, (Windows 7)
As I'm using a small SSD some of my folders were linked to HDD, they were ; Desktop, documents, app data, and many more from /user/
once I started my PC I had lost everything on my 2nd HDD and this was affecting my OS, all desktop icons were gone, many can't find X,Y,Z ... .exe autoruns
I did a scandisk on the affected HDD on another computer and it repaired many errors,
Here are the scan/repair results and showing the drive had used space while showing nothing on the drive.
Scandisk results (screenshots)
Then I did my best to match the gibberish named Found872653 folder to their corresponding directory.
My desktop icons are back and I recovered most of my data,
Windows must have deleted many entry when it saw the files were not available.
itune is broken
backgroung image is gone, (while it was on c:)
about 10 autorun are gone from registry
My custom taskbar with 25 quicklauch in C:\Users\Administrator\AppData\Roaming\Microsoft\Internet Explorer\Quick Launch was deleted.
every day I find 3-4 new things that doesn't work like before....
Who's fault ?
1st Kaspersky clearly messed the partition, (the linux logs show it had trouble unmounting the drive.)
2nd Maybe MSFT ... who deleted links and had trouble repairing symlinks