ok, that might be where the issue is coming from.
I just did a test export with a chapter I have with endnotes using the Endnotes feature both with the normal import and with the static text import and added a superscript character style to the numbers on both. I’m looking at the HTML and CSS and it appears with the standard import it doesnt retain the superscripted character style in the endnotes section but you have live links to your endnote numbers in the text. The static text import retains the superscripted character style but does not link to your endnote numbers in the text. I dont know why InDesign is overriding that character style on Export, looking at the code it really shouldnt be a problem to implement, each number has two character styles applied to the anchor tag that arent even in the stylesheet (so basically they’re unused), by simply adding vertical-align:super; to one of the classes it superscripts them.
Anyway, sorry that took a little tangent into the HTML and CSS. But off the top of my head I dont know of a work around in InDesign to keep the numbers superscripted on export since it appears that they are overriding character styles, well, besides going into the HTML and CSS itself and adding it by hand.
Hope that made sense, I might submit this to the InDesign feedback page because it really shouldnt override superscripting on ePub Export.