[lumpynose]

I haven't tested this yet but my current strategy is, in the body text have

blah blah.<a id="backref1" href="#note1">[Note 1]</a> Blah blah blah

Then the footnotes are at the end of each chapter:

  <section class="endnotes">
    <header>
      <h3>End notes</h3>
    </header>

    <ol>
      <li> <a id="note1" />Hannibal, Missouri. (<a href="#backref1">Return to previous place.</a>)</li>
    </ol>
  </section>

Edit; hit the reply button too quickly.

I just discovered that the Kobo doesn't properly format description lists; dl/dt/dd. So I definitely need to see if it handles ordered lists correctly. If it doesn't then I'll just use paragraphs:

<p><a id="note1" />Note 1: Hannibal, Missouri. (<a href="#backref1">Return to previous place.</a>)</p>

Edit 2: I forgot to say that from what I've read the links using the A tag work better when the target (end note in this case) is in the same file.