My user has 0 MB used out of -1 MB in unlimited files.
Disk Quota shown much more than it actually is in file manager.
This problem is caused by broken web server disk quota.
Log into the web server as root:
Turn off disk quota:
quotaoff [hsphere_partition] * /hsphere/ usually
Go to H-Sphere partition and remove files aquota.user and quota.user:
cd [hsphere_partition] rm -f aquota.user quota.user
Update aquota.user and quota.user files:
quotacheck -m [hsphere_partition] * ignore "-m" for Free BSD
Turn on disk quota:
Then log into CP server as root and change to cpanel user:
su - l cpanel
Reset user defined quotas:
java psoft.hsphere.tools.SetQuota -lid [logical_server_id]