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If I understand the problem correctly, there are NO links associated with the footnotes in question. The only problem is the appearance of the footnotes themselves in the text. If that's correct, try the suggested CSS for the footnote numbers themselves. I think it might still solve your problem.
Of course, you will have to enclose each footnote number inside a <span class="SUPERSCRIPTRef">whatever</span>. The CSS solution was intended only to correct the appearance problem, not hyperlinks. And of course you can adjust the parameters of the CSS definition to suit your purpose.
Albert
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