Have you double checked the code in the ePub to see how clean it is? Sometimes converting from Mobi can be a real mes before it's put up for sale.
Besides, why are you using InDesign if you don't know how to use it? You should be using it to create the ePub. Not having Calibre do it from an inferior format. That means that any ePub features that would be used when making the ePub properly, will be lost. So what you are doing (very possibly) is giving your customers and inferior product.
I told you what endnotes are and where the go. Just spend the time moving them so they are endnotes and not footnotes and you can create the ePub from there.
Last edited by JSWolf; 08-21-2012 at 07:48 PM.