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In product configuration, what is the purpose of Send Transaction Data to a URL option?

If edited, does it affect the add to cart code?

That option is if you want our service to transmit order data to some outside URL after payment has been completed, say to a third-party service such as a drop-shipper, or to some script you have developed on your own server, for further post-purchase processing. It does not affect the cart button codes we provide. See our help page here for further details:
http://www.e-junkie.com/ej/help.integration.php

As a general rule, it's safe to assume that if you don't recognize what a particular setting is for, you probably don't need to concern yourself with it. We have added so many settings to meet specific needs, that you can easily feel overwhelmed trying to understand them all when in fact most of them will not be relevant to your situation. Focus instead on the end results you want to accomplish, then look for information on what settings will help you meet that goal, such as our help pages indexed here (also under the "help" link in blue on our main Sellers pages :^):
http://www.e-junkie.com/ej/help.php

You can always also post a question here about what you're trying to set up, so anyone can see your inquiry and post a reply of benefit to others, or send us a private support request via email here (also linked in red at the top of all our site pages :^):
http://www.e-junkie.com/ej/contact.php