Usually when you delete a large amount of data from your email accounts or your client's accounts, the amount of space those emails occupy doesn't update instantly.
Usually this takes place after a few hours and a few cron jobs execution (already implemented during the installation of cPanel/WHM on your server.)
If you need to update that disk space faster, perhaps because the user is getting an over quota warning, you can try the following:
/scripts/generate_maildirsize --verbose --allaccounts --force --confirm
