Are you telling us that Mchk has a hidden feature of automatically enabling protection on all mailboxes? Because by default it doesn't enable it on all mailboxes and you have to do it one by one.
Mchk is an internal utility intended for use by Plesk Control Panel. However, as administrator, you can use it for restoring the Qmail and Courier-imap configuration by internal Plesk database when needed. By default mchk is running in the background mode, to execute it in the foreground, use the -v option.
Example: /usr/local/psa/admin/sbin/mchk -v
Note
You may not wish to restore SpamAssassin settings for mail accounts, as it requires running Perl interpreter. To speed up restoring the use --without-spam option."
I had to type the above text from the Plesk manual by hand because cutting and pasting from the PDF does not work, it gives blank characters.