– When you check the disk space used for an email account from cPanel, do you see a value very much different from the actual value ?
Verify the actual disk-space as :
# du -sch ~home/x.com/mail/x.com/user/
This issue happens when cPanel disk usage variable is not functioning
correctly.
– Usually a upcp ( /scripts/upcp --force ) would fix it.
If it doesnt or if you are not in a state to update cPanel, you can fix this issue by running the below command :
# /scripts/generate_maildirsize --confirm --allaccounts --verbose $user
$user = cPanel account name which is having this issue.
If the above too does not help, then log out from cPanel and
delete the email_accounts.yaml and email_accounts.cache files from the account’s “.cpanel” folder.
These files will automatically be created the next time you log into cPanel.
cd ~username/.cpanel
# rm email_accounts.yaml
# rm email_accounts.cache
This should clear the issue.