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Shared hosting cPanel says:

10,564.19 MB total disk space used.      
20,000.00 MB quota limit (4,084.34 MB used).

These figures may not reflect recent changes to your account’s disk usage.

The Disk Usage table below indicates how much space the directories’ contents use, not how much space the directory itself uses. Files typically occupy more disk space than their actual size. This may cause discrepancies between the data you see in the File Manager versus the information you find here.

10,564.19 MB total disk space used != 4,084.34 MB used

How do I reclaim the 6GB? Can I defragment the server's HDD?

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    I cannot speak for cPanel or your scenario, however, often the numbers do not line-up when checking for how much disk space is used. It is almost always usage versus allocation. For example, an empty file, 0k, is likely 4k allocation plus space in the index and directory file. So you may be taking about 5-6k. When the numbers are far apart, it is often due to a large number of files and/or directories. As well, some files when created allocate a much larger chunk of space with less used. Some database files are famous for this. Cheers!! – closetnoc Jun 24 '16 at 14:29
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15 minutes after I posted this I received a reply from hosting support saying:

Total disk space used = ~4GB, instead of 10,564.19 MB,

so it appears there is a delay until cPanel catches up with changes in disk space usage.

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