This is really driving me up the wall now.

Randomly, all my menu items for all menus are just being deleted on their own. Not the menus themselves but all items within them.

This is a custom theme we built upon the Bones boilerplate. We've built plenty of sites on Bones though and we're not experiencing the problem with any others.

I know the usual advice will be:-

 - Deactivate all plugins and see if the problem persists.
 - Revert to the default Wordpress theme and see if the problem persists.

But this isn't particularly practical as it means breaking our website for weeks on end waiting to see whether the problem occurs again.

Each time this happens, we have to manually rebuild all our menus and it is becoming a real pain now plus potentially catastrophic if Google crawl our website when these menu items have all been deleted.

This only started happening since the 3.8 update but occurs within four days of reinstating all the menu items again.

There is nothing of note in the error logs. This last happened in the past 48 hours and all we have in the error log from this period is the following (actual domain replaced with `domain.com`):-

    [Sun May 25 02:32:23 2014] [warn] RSA server certificate CommonName (CN) `plesk' does NOT match server name!?
    [Tue May 27 04:10:55 2014] [error] [client 188.143.234.90] script not found or unable to stat: /var/www/vhosts/domain.com/cgi-bin/php
    [Tue May 27 04:10:55 2014] [error] [client 188.143.234.90] script not found or unable to stat: /var/www/vhosts/domain.com/cgi-bin/php5
    [Tue May 27 04:10:55 2014] [error] [client 188.143.234.90] script not found or unable to stat: /var/www/vhosts/domain.com/cgi-bin/php-cgi
    [Tue May 27 04:10:55 2014] [error] [client 188.143.234.90] script not found or unable to stat: /var/www/vhosts/domain.com/cgi-bin/php.cgi
    [Tue May 27 04:10:55 2014] [error] [client 188.143.234.90] script not found or unable to stat: /var/www/vhosts/domain.com/cgi-bin/php4
    [Tue May 27 04:10:55 2014] [error] [client 188.143.234.90] script not found or unable to stat: /var/www/cgi-bin/cgi_wrapper/php

If all anyone can suggest is the above bullet points, then all I can really think of is to replicate the website in a dev environment and noindex the site for web crawlers (I've asked in various communities already) - there does seem to be a few other people that have experienced the same problem with little idea of resolution although for some it seemed to be related to plugins (although I don't have those plugins installed on our website).

Frustrating! Can anyone shed some better light on how to get to the bottom (debug) of this one?