WP-CLI not recognizing commercial plugin updates

What you experienced may be some network level problem or someone temporary removed the download resources. For instance before the update.

Most of the details you can get from the source code https://github.com/wp-cli/wp-cli.

Plugin update function in there looks like this.

function update( $args, $assoc_args ) {
        if ( isset( $assoc_args['version'] ) ) {
            foreach ( $this->fetcher->get_many( $args ) as $plugin ) {
                $assoc_args['force'] = 1;
                $this->install( array( $plugin->name ), $assoc_args );
            }
        } else {
            parent::update_many( $args, $assoc_args );
        }
    }

And when you specify wp plugin update --all it actually goes through the
parent::update_many function, where the parent is actually CommandWithUpgrade class.

Bottomline, wp-cli uses resources provided by plugins like this:

# Install from a remote zip file
wp plugin install http://s3.amazonaws.com/bucketname/my-plugin.zip?AWSAccessKeyId=123&Expires=456&Signature=abcdef

But there you can see the information you should not see.

Sidenote

Please note that some premium plugins does not support being upgraded via WP-CLI. E.g. I know BackupBuddy and Gravity Forms works fine, but the plugins from Yoast does not. This may change.