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

This can be done with Plesk mchk utility:

# /usr/local/psa/admin/sbin/mchk --help
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/*).

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

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