Hi,
The links in the emails are generated in the preload section of the emails that you can find when you edit them via the menu System > Emails.
It's done by this code:
if(empty($customer->user_cms_id))
$file_pos .= '&email=' . $customer->user_email;
$oid = $data->order_id;
if(!empty($data->cart->order_parent_id))
$oid = $data->cart->order_parent_id;
$t .= '<a href="'.hikashop_frontendLink('index.php?option=com_hikashop&ctrl=order&task=download&file_id='.$file->file_id.'&order_id='.$oid.$file_pos.$url_itemid).'">'.$fileName.'</a><br/>';
You would have to change it to something like that:
if(empty($customer->user_cms_id))
$file_pos .= '?email=' . $customer->user_email;
$oid = $data->order_id;
if(!empty($data->cart->order_parent_id))
$oid = $data->cart->order_parent_id;
$t .= '<a href="'.hikashop_frontendLink('index.php?option=com_hikashop&ctrl=order&task=download&file_id='.$file->file_id.'&order_id='.$oid.$url_itemid).$file_pos.'">'.$fileName.'</a><br/>';
And that should fix the problem.
But you need to be sure to have the SEF activated, otherwise you will have two "?" in the URL and it won't be valid anymore.
Regards,