This code will upgrade ACF to allow for multi-item reverse loopkup by giving each relationship connection a 'rel_$post_type' meta_key with a serialized array of posts containing the post_ids of the originating post.

acf.php

// Added "before_delete_post" action to trigger rel_cleanup (cleans up all associated posts with rel_ meta_keys when a post is deleted)
function Acf()
{

	// vars
	$this->path = plugin_dir_path(__FILE__);
	$this->dir = plugins_url('',__FILE__);
	$this->version = '3.3.9';
	$this->upgrade_version = '3.3.3'; // this is the latest version which requires an upgrade
	$this->cache = array(); // basic array cache to hold data throughout the page load
	
	
	// set text domain
	load_plugin_textdomain('acf', false, basename(dirname(__FILE__)).'/lang' );
	
	
	// controllers
	$this->setup_controllers();
	
	
	// actions
	add_action('init', array($this, 'init'));
	add_filter('post_updated_messages', array($this, 'post_updated_messages'));
	add_filter('manage_edit-acf_columns', array($this, 'acf_columns_filter'));
	
	add_action('admin_menu', array($this,'admin_menu'));
	add_action('admin_head', array($this,'admin_head'));
	
	add_action('wp_ajax_get_input_metabox_ids', array($this, 'get_input_metabox_ids'));
	add_action('before_delete_post', array($this, 'rel_cleanup'));
	
	return true;
}

/*
*  rel_cleanup
*
*  @description: Cleans up any reverse relationships when you delete a post.
*  @since ...
*  @created: 30/08/12
*/

function rel_cleanup($post_id) {
	$meta = get_post_custom($post_id);
	$acf = get_post_custom_keys($post_id);
	if( $acf ) {
		foreach($acf as $field_name) {
			if( strpos($field_name,'_') === 0 ) {
				$field = get_post_meta($post_id, $field_name, true);
				$field_id = $this->get_post_meta_post_id($field);
				if( $field_id ) {
					$field_meta = get_post_meta($field_id, $field, true);
					if( $field_meta['type'] == 'relationship' ) {
						$name = str_replace('_','',$field_name);
						$rel_items = maybe_unserialize($meta[$name][0]);
						acf_Field::update_rel( $post_id, $rel_items );
					}
				}
			}
		}
	}
}

acf_field.php

// Creates the 'rel_$post_type' meta to store the reverse lookup
function update_rel( $post_id, $items ) {
	if( $items ) {
		global $post_type;
		foreach($items as $rel_id) {
			$current = get_post_meta($rel_id, "rel_$post_type", true);
			if( !empty($current) ) {
				$item = array_search($post_id,$current);
				unset($current[$item]);
				if( !empty($current) ) update_post_meta($rel_id, "rel_$post_type", $current);
				else delete_post_meta($rel_id, "rel_$post_type");
			}
		}
	}
}

function update_value($post_id, $field, $value)
{
	// strip slashes
	$value = stripslashes_deep($value);
	
	// Setup reverse lookup
	if( $field['type'] == 'relationship' ) {
		global $post_type;
		// Get the current related posts
		$related_current = get_post_meta($post_id, $field['name'], true);
		
		// If we are saving any values and already have saved related posts, do a diff to see if any related posts are being removed
		if( $value && $related_current ) $remove = array_diff($related_current, $value);
		else $remove = $related_current;
		
		// If we are removing posts then loop through them and update/delete the related post's rel_ meta.
		if( $remove ) self::update_rel( $post_id, $remove );
		
		// For all values left over create new or update the meta for the related post only if the value isn't currently there.
		if( $value ) {
			foreach($value as $rel_post) {
				$current = get_post_meta($rel_post, "rel_$post_type", true);
				if( $current ) {
					$search = array_search($post_id,$current);
					if( $search === false ) array_push($current,$post_id);
				}else $current = array($post_id);
				update_post_meta($rel_post, "rel_$post_type", $current);
			}
		}
	}
	
	// if $post_id is a string, then it is used in the everything fields and can be found in the options table
	if( is_numeric($post_id) )
	{
		update_post_meta($post_id, $field['name'], $value);
		update_post_meta($post_id, '_' . $field['name'], $field['key']);
	}
	else
	{
		update_option( $post_id . '_' . $field['name'], $value );
		update_option( '_' . $post_id . '_' . $field['name'], $field['key'] );
	}
	
	
	//clear the cache for this field
	wp_cache_delete('acf_get_field_' . $post_id . '_' . $field['name']);
	
}