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#1
Pay no attention to that.
Computing the size of a directory is more than just adding file sizes
How can I find out how much disk space the WinSxS folder is really occupying?
How come Explorer reports higher disk space used on my volume than my third party disk space tool?
Bottom line: You cannot use File Explorer to get an exact reading on free space or space used.
I shall stick my neck out here: those articles by Raymond Chen highlight the issues, but he never states that Explorer gets the size of a complete partition wrong. He does state that "Explorer obtains information about used and free disk space by calling Get*Disk*Free*Space*Ex, so the information comes straight from the file system. "
In my experience, Explorer's 'used' value for a partition matches very closely that of Wiztree, which is aware of hard links (and maybe other complications), and I am inclined to believe it. Explorer does fail when it comes to individual folders (it usually over-estimates). If the OP were to look at his C: with Wiztree, he (and I) may learn something - but I am ready to be proved wrong.
Added: the OP might also check what Disk Management says.