[repilo]

Originally Posted by DNSB

Perhaps instead of using header tags in your footnotes, you could use appropriately styled p tags?

I don't quite understand what you mean. So I'm going to detail it a bit more.
File 07.xhtml:

<h1>Header</h1>

  <p>Text.<a id="rf24" href="notes.xhtml#nt24"><sup>[24]</sup></a></p>

<h2 id="sigil_toc_id_39">Header</h2>

  <p>Text.<a id="rf25" href="notes.xhtml#nt25"><sup>[25]</sup></a></p>

File notes.xhtml:

  <div class="nota">
    <p id="nt24"><sup>[24]</sup> Text. <a href="07.xhtml#rf24">&lt;&lt;</a></p>
  </div>

  <div class="nota">
    <p id="nt25"><sup>[25]</sup> Text. <a href="07.xhtml#rf25">&lt;&lt;</a></p>
  </div>

Footnote 24 (and previous footnotes) is shown in popup window; footnote 25 (and following footnotes) is not.
For some reason, only footnotes above <h2 id=“sigil_toc_id_39”> (at least in this particular case) are shown in popup.
If I move footnote 25 above said h2, then it shows in popup.
If I rebuild the table of contents only up to level 1 (i.e. not including h2), all footnotes are shown in popup.