Just FYI, if you are the network admin and have created an account via regular username, then activated an email login plugin and this plugin, this plugin will change your username on your profile etc., but not in the site_meta table, which is where WP looks for the network admin.
So your username will fail to log you in after the change, but the email will work. BUT, WP is still looking for the username in wp_sitemeta to authenticate you as the network admin, so the Network Admin option disappears from the Site Admin panel and you're stuck.
My fix was to use phpmyadmin to open the wp_sitemeta table and change the username in the site_admins field to be the email address, + change the s: number to match the number of chars in the email instead of the username (that's what the s: number value is in that field, the number of chars). Voila, log in with email and there's the Network Admin option again.
This post is just FYI if anyone else finds themselves with this problem. True to the plugin's docs, nothing happened until I updated my profile, and by then I'd forgotten all about that little detail, so I was completely stumped :)