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I've done that. Run Chkdsk and no problems found.
Try WizTree, it often can show files that TreeSize and WinDirStat can't display.
It's free, they have a portable version, and it runs fast.
Antibody Software - WizTree finds the files and folders using the most disk space on your hard drive
This all started with 10 needing more space than Microsoft stated. I cloned the original drive and adjusted the space accordingly. I had problems but finally got it to boot to but my drive letters for; D (Program Files), E (Documents), Y (Temp) and Z (BackUps) are moved around to; F (Program Files), G (Documents), D (Temp) and E (BackUps). I can access Control Panel but I can't access any Command Prompts, Regedit or Device Manager even though C:\ is the Windows drive. I get a message that "Windows cannot find C:\Windows\System32\diskmgmt.msc when I try to access Disk Management. I tried right clicking and opening properties and locating it manually and I get the same message. I've tried changing the drive letters from the Command Prompt using 10's install disk and Advanced under repairs. I've tried using Falcon Four UBCD and accessing the Registry from it. Neither one works. So I'm going to start another thread so see how I fix this.
Run "Windows Disk Cleanup", select "clean up system files" it'll have a little shield next to it, look for "previous windows installations" and see how much space it is taking up. Along with system error memory dumps. You can delete both right there if you want. the "previous windows installations" is, i believe, an image that you can fall back on but you can just create a new one right after. Windows will also get rid of that "previous windows installations" after one month. Hope it helps a little.