If you had disabled IPN previously, you may need to re-enable IPN with PayPal, but our standard button code should take care of that automatically, as long as you follow our PayPal integration instructions:
As noted there, you should set Auto-Return: Off. The only reason you would set that "on" is if you are also using PayPal to take payments for other sales unrelated to your E-junkie products, so in that case you should also set Payment Data Transfer: On, and set the Return URL to whatever you require for your non-E-junkie sales.
If you are able to resubmit the IPNs from your PayPal IPN history, go ahead and do so, but otherwise you may need to fulfill your buyer's orders manually for those transactions that were not successfully completed. You can use your Seller Admin > "Send free download link" to issue download links manually.