How do I repair/rebuild all mail configuration files and restore settings for all mailboxes?

Resolution
This can be done with Plesk mchk utility:

# /usr/local/psa/admin/sbin/mchk --help
Synopsis:
mchk [OPTION]
--without-spam - restore all settings except for SpamAssassin configuration
--with-spam - restore all settings
--spam-only - restore only SpamAssassin settings

This utility rebuilds in line with Plesk database Qmail control files in the /var/qmail/control, /var/qmail/users directories and mail users’ settings. Also, it sets proper ownership/permissions for all mailboxes (/var/qmail/mailnames/*).

Example:
# /usr/local/psa/admin/sbin/mchk --with-spam

cPanel email inconsistent quota !

If a cPanel email user quota does not match what is being reported by the system or a mail client run the following to determine how much space has been used for real:

du -hs /home/username/mail/userdomain.com/user/

then compare it with what cPanel reports for the disk usage, if they are different delete:

/home/username/mail/domain.com/user/maildirsize

finally re-login to cPanel and it should be resolved.

Error 550 – “The recipient cannot be verified” – cPanel

On servers running cPanel, you may find that mail sent to valid users it bounced back by your mail server. The bounce back messages will be similar to the following.

PERM_FAILURE: SMTP Error (state 9): 550-"The recipient cannot be verified. 
Please check all recipients of this550 message to verify they are valid.
If this is occurring, you will need to check your exim_mainlog file for entries 
similar to the following.
H=(nf-out-0910.google.com) [IP] F=<[email protected]> rejected RCPT 
<emailAccount@domainName>: No Such User Here
If you are sure that email account does indeed exist, you will need to run the 
following commands to correct the issue.
/scripts/updateuserdomains
/scripts/mailperm 
You will then also need to check your /etc/localdomains file and verify that the 
domain name is present. Also verify that the DNS line in your 
/var/cpanel/user/username contains the domain as well.