I've updated our help page for customizing thank-you pages to be clearer about what the customization does and doesn't replace:
The standard thank-you page we generate for you will include a bullet-pointed list of items in the buyer's order (including links for downloadable items), then the following default message will also be shown on any non-customized thank-you pages we generate for you:
I.e., whatever you place in the Message (HTML) field of a product's settings will be added to (not replace) the product's name and download link on your E-junkie-generated thank-you pages. See the example provided at the bottom of that help page to get a clearer idea of which customizations get inserted where on the thank-you page.
You may also want to disable the product-specific thank-you emails (in each product's settings, tick Enable Templated Email but leave the Email Message field blank), so buyers would only get your Common Thank-you Email message with a link to the consolidated thank-you page for all items in their order, in case they did not proceed to that page directly following checkout.