Wow, that's ridiculous. On my Nook Touch, the back button doesn't disappear after a few seconds, but it does disappear if I turn the page, which is annoying if the footnote continues onto the next page. However, the footnote link does go back to the original position, as others have noted. This will make the "back" button pop up at the top of the page again, but if you swipe down from the top of the screen to the bottom, it will make everything except the text (including title, time, menu buttons, highlights, etc) go away.
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