Sorry, I am not sure if I follow - are you saying Calibre conversion makes it so that footnotes are not visible on the same page? Anyway, I uploaded a book with no conversion (attached), and footnotes are not showing on the same page either - but the html code is different too:
Code:
<sup><a id="przypis6_1" href="footnotes_39.xhtml#opis_przypisu6_1">[1]</a></sup>