I've figured it out. To make the inline footnote works, must put the footnotes in the "Footnotes" section. Here is the example:
I have the file: "HDN is the best.html"
<title>HDN is the best</title>
<h1>Best of HDN</h1>
<p><sup><a id='fs-1' ...
If you are starting with an .epub file, there is an editor program in the Calibre suite which can change anything in the .epub, including the fonts:
But if you convert the file from .epub to .mobi, with any program including Calibre, it's then almost impossible to edit the resulting .mobi file. So you get stuck with ...
First, I don't have any insight into CLI calibre and you might get a better answer from Mobileread or by posting a bug, but my guess is that the # character must be reserved exclusively for fragment identifiers for HTML. So it is most likely a feature, not a bug.
Think about it. If the file name were allowed to contain a #, then you would not be able to ...
Converting from mobi to pdf is almost always going to be a problem. Both are rendered formats. The problem could come from anywhere. Two ideas:
First, try to obtain an epub copy instead of a mobi file. It's easier to convert from epub to pdf than from mobi to pdf.
Try decompiling the mobi file (go to mobileread to find a tool that can do so).