It can take 15 minutes for CPanel to update the File Usage value after deleting files.
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In CPanel go to Files -> File Manageror use a FTP client such as FileZilla
We recommend downloading FileZilla from here.
If you are behind a router enable "passive mode" in the preferences of your FTP program.
Go into your ftp options and see if passive mode is checked. If it is, uncheck it. If it is not...
You can password protect directory's within cPanel.In cPanel go to Files -> Directory Privacy