I was searching for a long time to resolve a strange problem on several WordPress sites, where menu items were mystically disappear without any cause. Today I’ve realized that all of them have Stealth Publish plugin, which I like very much. But it hasn’t been updated for about half year. So I searched for issues with this plugin and have found that indeed this plugin is leading to weird menu items removal.
A workaround, if you don’t want to remove this very useful plugin, is suggested on StackExchange to be inserted into
/* Disable wp-cron to prevent menu from getting deleted */ define('DISABLE_WP_CRON', true);
Now I hope this problem will not be back 🙂