We would like to have our master (parent) Main WP installation behind htpasswd protection set up on root HTTP folder. However, when we do that, Main WP can no longer perform updates on child sites. It does still see child sites and is connected to them, but it cannot perform updates or installs on them.
You can use our free Dashboard Lock extension to lock down the Login page or the WP Admin area.
Doing so won’t interfere with the MainWP functionality.