I found out that Windows calculates much more used space on my 128GB SSD than the total volume of all files on it. WinDir calculates only 62.4GB even with junction point following, but Windows shows an used size of 87.8GB, 40% more!
I found a few questions on cases like this, but none of them provided the good answer to me:
What could be the cause? Is there any way to reclaim that 25GB space of mine?
(System: Windows 10 only, 128GB SSD + 1TB HDD, user folders natively moved to the HDD. If you need any other details, ask for it.)
Answer
The answer is simple, as @Daniel B pointed out: Run WinDirStat as Administrator. Since I assumed it does so by default, I haven't, so it couldn't count about 25GB file in other users' folder.
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