WHM is showing incorrect disk usage details and I can't change the quota via WHM

The problem happens when the disk quota file get corrupted on server. You can run the following command while logged into the server as root.

/scripts/fixquotas –force

It may give errors like the following, if the problem is not solved completely.

Resetting quota for abcde to 500 M
edquota: Quota write failed (id 32230): Invalid argument
Resetting quota for xyz to 500 M
edquota: Quota write failed (id 32010): Invalid argument

In that case, a quick reboot of the server will help to solve the problem. You may restart the server via SSH using the command shutdown -r now.