Index: src/wp-admin/network/upgrade.php
===================================================================
--- src/wp-admin/network/upgrade.php	(revision 38350)
+++ src/wp-admin/network/upgrade.php	(working copy)
@@ -55,7 +55,17 @@
 			update_site_option( 'wpmu_upgrade_site', $wp_db_version );
 		}
 
-		$blogs = $wpdb->get_results( "SELECT blog_id FROM {$wpdb->blogs} WHERE site_id = '{$wpdb->siteid}' AND spam = '0' AND deleted = '0' AND archived = '0' ORDER BY blog_id DESC LIMIT {$n}, 5", ARRAY_A );
+		$args = array(
+			'spam' => '0',
+			'deleted' => '0',
+			'archived' => '0',
+			'network_id' => $wpdb->siteid,
+			'number' => $n,
+			'fields' => 'ids',
+			'order' => 'DESC',
+			'orderby' => 'id',
+		);
+		$blogs = get_sites( $args );
 		if ( empty( $blogs ) ) {
 			echo '<p>' . __( 'All done!' ) . '</p>';
 			break;