Thanks for the tips.
On line 971 the original confirm.php page has
$WA_redirectURL = "checkout_success.php";
when removing the checkout_success leaving $WA_redirectURL = ""; it allowed for both the order confirmation to be displayed on the store site and for an email confirmation to be sent.
On a replica site this causes the cart.php page to be displayed. When reinserting the original line (971) the confirmation (checkout_success.php) page is displayed however the confirmation of order email is not being sent which was the original reason for modifying the confirm.php page.
Haven't found any other issues at this stage and haven't made any other modifications from the working store site. Any other suggestions?