Hi,
Normally, you have the "order creation notification" email which is sent when the order is created, and the "order status notification" email which is sent when the order is confirmed.
As you have two different emails, if you only modify one, you won't see the change in the other one.
So if you only want to add some text when the order is confirmed, you can edit the order status notification in the menu System>Emails and in the preload area, you can replace the code:
'ORDER_BEGIN_MESSAGE' => JText::sprintf('THANK_YOU_FOR_YOUR_ORDER_BEGIN', HIKASHOP_LIVE),
by:
'ORDER_BEGIN_MESSAGE' => JText::sprintf('THANK_YOU_FOR_YOUR_ORDER_BEGIN', HIKASHOP_LIVE). 'If it contains electronic material, you can now download that electronic material by clicking on the order number (above) to return to the site and download your order. Physical items will be shipped soon. If this is for a quote, Someone will reach out on the next US business day.',