Fixing already provisioned VMs
What about VMs already provisioned? First, the container must be powered off, then issue the vzctl set “VMID” –quotaugidlimit 1000 –save. Note that “VMID” is a placeholder for the container ID. Then start the container and you will have the second quotas enabled for use.
Fixing cPanel Quotas
Once you have the quotas enabled you will want to manual force cPanel to refresh the quotas. I would suggest running vzctl enter “VMID” to simply gain access to the VM. Again “VMID” is a placeholder for the container ID. Once inside the VM run the cPanel /script command to force the recheck on quotas /scripts/fixquotas You should see it force a recheck and will print out all of the quotas the accounts are getting set to. Once you see this you are finished,and cPanel is now showing disk usage correctly.