Why does the email disk usage in cPanel not match the disk usage shown with the du command?

Question

Why does the email disk usage in cPanel not match the disk usage shown with the du command?

Answer

Dovecot saves disk space by hardlinking identical messages. When significant hardlinking occurs, the email disk usage reported in the cPanel interface can differ significantly from what you see when using the du command. The cPanel interface is not hardlink-aware and counts each message as if it were not a hardlink. 

The du utility is hardlink-aware and reports the actual disk usage by counting the disk usage of the hardlink and not the references. Using the -l or --count-links option with the du command will cause du to count each hardlink as if it were not a hardlink:

# du -hs --count-links /home/user/mail/domain.tld/user

Note: You want to replace /home/user/mail/domain.tld/user with the path to the email address.

Additional Resources

Maildir Configuration: maildir_copy_with_hardlinks