functions.php

<?php
/*
Plugin Name: Convert SMURF to CMB2 repeatable field groups
Plugin URI: http://www.iweb.co.uk/
Description: Go through and zero index each SMURF array.
Version: 1.0.0
Author: iWeb
Author URI: http://www.iweb.co.uk/
*/

if ( isset( $_GET['fix_smurf'] ) ) {
	add_action( 'template_redirect', function () {
		global $wpdb;

		$results = $wpdb->get_results(
			"
			SELECT pm.post_id, pm.meta_value FROM {$wpdb->postmeta} pm
        	LEFT JOIN {$wpdb->posts} p ON p.ID = pm.post_id
        	WHERE pm.meta_key = '_cmb_specifications'
        	"
		);

		if ( empty( $results ) ) {
			die( 'No post meta with that key.' );
		}

		foreach ( $results as $result ) {
			printf( 'Working on post ID %s:<br>', $result->post_id );
			$meta_value = maybe_unserialize( $result->meta_value );
			$fixed_meta_value = array_values( $meta_value );
			update_post_meta( $result->post_id, '_cmb_specifications', $fixed_meta_value, $meta_value );
		}

		die( 'Done.' );
	} );
}