No, even if you have a dedicated IPN configured for something else, E-junkie will not be affected by that. Our purchase buttons/links automatically transmit our IPN requirements to PayPal with every checkout, which would override your PayPal account's manual IPN settings for any orders coming from our system.
If you still need to send IPN to a custom/third-party URL even for your E-junkie orders, our IPN-style webhook integration feature may satisfy that need for you.
The only time we require you to specify our IPN URL manually is when you are selling on a site where you can not use E-junkie purchase buttons/links to initiate the sale.
If you or PayPal have disabled IPN for your PayPal account, you may see IPNs for your E-junkie transactions are Disabled in your PayPal account's IPN History. In this case, you may need to manually re-enable IPN in PayPal by going to [your name] > Account Settings > Website Payments > Instant Payment Notifications > Edit IPN Settings, where you should choose to Receive IPN Messages (Enabled) and enter this Notification URL: