Hi! I'm having a similar situation with Windows 10 64bit
I have an external drive, it is 5TB, formatted NTFS. I used to have this harddrive mainly to store my big photos collection (photos all the way back from 2005).
So I used to have the photos under folders, for example R:\Photos:\2005\ and inside that folder, there were other subfolders and inside those subfolders the photos of that time that were taken.
We are talking about a lot of Gigabytes of photos here. So one day, I realized that all files were literally gone, excluding the 2013, 2016 and 2017 folders. I never moved those folders, or deleted those. It is really really weird why those photos were gone. Now my drive is not old, so I doubt it has a hardware issue. But the USB 3 controller that the drive was hooked, had a wrong set of drivers installed (I realized that later on), so the wrong set of drivers didn't work very well with the drive, and could corrupt the filesystem of the drive. I remember a lot of times, that suddenly the drive wasn't mounted, and after a restart the Windows would try to repair the drive. Now what I believe is at the last CHKDSK of Windows, I lost my photos.
Now here comes the most interesting part: Scanning the drive with Recuva shows that there are ZERO deleted files. This is insane. How could the drive have ZERO deleted files? This is not possible.
So anyone had a similar experience? How would you approach such kind of behavior? I need to get my photos back (hopefully in directory structure).
I tried the advice with the shutdown command to rebuild USN but it didn't brought my files back.