If you are an InDesign (CC 2014) user planning to export a fixed-layout ePUB and you have footnotes in your document, you might be dissapointed to notice that there is no option to make these footnotes become popup notes using the ePUB3 standard epub:type.
In the export to ePUB(reflowable) options we can select the popup type, but not for the fixed layout. Your footnotes will remain exactly where they are – on the page. Dissapointing no?
InDesign will expect the footnotes to be in the same XHTML file where they are referenced. There are some settings in InDesign, but nothing will help us convert them to invisible notes that are only seen in a popup. Is there a solution while we wait for Adobe to release another version of InDesign?
You know an InDesign file is never finished, even if you do save it as 'Final version'!
Get real. You are going to want to go back to InDesign and re-export your ePub (reflowable), because someone noticed a typo or a badly captioned photo.
Can we, save ourselves a lot of bother by grabbing all those changes and slip them into the new version?
Here's how with InDesign CC (2014) — yes you gotta get the latest version.
Frankly, I am only dealing with re-flowable ePubs from InDesign. Not fixed-layout.