[Steven Zahm]

@ Christopher

Ok, all fixed up!

For reference for anyone else who has implemented this or wants to. Here’s the updated code snippet to get it to work again.

function cn_initial_search_filter( $posts, $WP_Query ) {
    global $wp_query;

    if ( ! class_exists('cnTemplatePart') ) return $posts;

    $shortcode = 'connections';
    $pattern   = get_shortcode_regex();

    // Grab the array containing all query vars registered by Connections.
    $registeredQueryVars = cnRewrite::queryVars( array() );

    foreach ( $posts as $post ) {

        // If we're in the main query, proceed!
        if ( isset( $WP_Query->queried_object_id ) && $WP_Query->queried_object_id == $post->ID ) {

            /*
             * $matches[0] == An array of all shortcode that were found with its options.
             * $matches[1] == Unknown.
             * $matches[2] == An array of all shortcode tags that were found.
             * $matches[3] == An array of the shortcode options that were found.
             * $matches[4] == Unknown.
             * $matches[5] == Unknown.
             * $matches[6] == Unknown.
             */

            if ( preg_match_all( '/'. $pattern .'/s', $post->post_content, $matches )
                && array_key_exists( 2, $matches )
                && in_array( $shortcode, $matches[2] ) )
            {

                // Parse the shortcode atts.
                $atts = shortcode_parse_atts( $matches[3][ array_search( $shortcode, $matches[2] ) ] );

                // Remove the cn-image query vars.
                $wp_query->query_vars = array_diff_key( (array) $wp_query->query_vars, array_flip( array( 'src', 'w', 'h', 'q', 'a', 'zc', 'f', 's', 'o', 'cc', 'ct' ) ) );

                // Show the just the search form w/o showing the intial results?
                // If a Connections query var is set, show the results instead.
                if ( isset( $atts['initial_results'] )
                    && strtolower( $atts['initial_results'] ) == 'false'
                    && ! (bool) array_intersect( $registeredQueryVars, array_keys( (array) $wp_query->query_vars ) )
                   )
                {

                    // Add return = true to $atts so template part are returned instead of echoed.
                    $atts['return'] = true;

                    // Enqueue the CSS and JS. We need to use the action because we're hooked 
                    // way to early in WP to use wp_enqueue_style() and wp_enqueue_script().
                    add_action( 'wp_enqueue_scripts', array( 'cnScript', 'enqueueStyles' ) );

                    // Add action to enqueue Chosen.
                    add_action( 'wp_enqueue_scripts', 'cn_enqueue_chosen' );
                    add_action( 'wp_print_footer_scripts', 'cn_init_chosen', 999 );

                    // Passing the shortcode $atts incase there are any template part specific shortcode options set.
                    $category  = cnTemplatePart::category( $atts );
                    $search    = cnTemplatePart::search( $atts );
                    $formOpen  = cnTemplatePart::formOpen( $atts );
                    $formClose = cnTemplatePart::formClose( $atts );

                    // Create the final output.
                    $replace = $formOpen . $category . $search . $formClose;

                    // All returns and tabs should be removed so wpautop() doesn't insert <p> and <br> tags in the form output.
                    //$replace = str_replace( array( "rn", "r", "n", "t" ), array( ' ', ' ', ' ', ' ' ), $replace );

                    // This needs to be wrapped in a div with an id of #cn-list so the CSS styles will be applied.
                    $replace = '<div id="cn-list">' . $replace . '</div>';

                } else {

                    // Rewrite the $atts array to prep it to be imploded.
                    array_walk( $atts, create_function( '&$i,$k','$i="$k=\"$i\"";' ) );

                    $replace = '[' . $shortcode . ' ' . implode( ' ', $atts ) . ']';
                }

                // Replace the shortcode in the post with something a new one based on you changes to $atts.
                $post->post_content = str_replace( $matches[0][ array_search( $shortcode, $matches[2] ) ], $replace, $post->post_content );
            }

        }

    }

    return $posts;
}

function cn_enqueue_chosen() {

    // If SCRIPT_DEBUG is set and TRUE load the non-minified JS files, otherwise, load the minified files.
    $min = defined('SCRIPT_DEBUG') && SCRIPT_DEBUG ? '' : '.min';

    wp_enqueue_script( 'jquery-chosen', CN_URL . "vendor/chosen/chosen.jquery$min.js", array( 'jquery' ), '1.1.0', true );
}

function cn_init_chosen() {

?>

<script type="text/javascript">/* <![CDATA[ */
    jQuery('select[name^=cn-cat]').chosen();
/* ]]> */</script>

<?php

}

add_filter( 'the_posts', 'cn_initial_search_filter', 1000, 2 );

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