To Fix Common reasons for quota problems
Run the following command as root user.
/scripts/fixquotas
Try finding other files owned by the user.
find -user username > /tmp/username.txt
This will list all files owned by this user that could be affecting the quota reported by Cpanel.
Cpanel/WHM sometimes has problems with the user quota files causing all users accounts to have unlimited disk space available or 0 megs of disk space in use.
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