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It's possible that Aquile is the problem. How many reading systems have you tried it with? Sigil doesn't really have any control over whether or not valid links are not clickable on various readers. Not all readers are as spec compliant as they should be. If your footnotes are working with Adobe's RMSDK, then I suspect they should work in any reputable reading system. I've not heard of Aquile before, so I can't comment on its reputation.
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