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I have checked that deleted files are still in use by the command

sudo find /proc/*/fd -ls | grep '(deleted)'

And I have been able to check for deleted files that are still in use. Why does this occur? Is there any way to delete them permanently?.

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As explained by Eliah Kagan in the comments, if a process has file open, it shall remain in memory even if file is unlinked from the filesystem. The simple approach is to reboot, since /proc is a virtual filesystem and its contents don't remain on the hard drive