I bet the issue is caused because the code is using the virtual function for include files rather than require_once:
try changing lines 5 - 9:
<?php virtual('/Connections/myCon.php'); ?>
<?php
//WA Database Search Include
virtual("/WADbSearch/HelperPHP.php");
?>
to:
<?php require_once('Connections/myCon.php'); ?>
<?php
//WA Database Search Include
require_once("WADbSearch/HelperPHP.php");
?>
to prevent this from happening again in the future, change the setting in your site definition for "Create Links Relative to" from "Server" to "Document"