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Oops. I just noticed my href= tags in what I posted earlier are for ids local to that file. If there aren't too many footnotes, I usually pull them up so that the actual footnote is just below the paragraph where they're called. So, I can get away with href="#fnnumber". If your actual footnotes are in another file/chapter, then your hrefs should look like href="filename#fnnumber". Once you start typing after the initial quote mark, the Calibre editor should just pop up likely candidates that you can click on with your mouse.
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