What Calibre does is check what each font is going to be displaying. So when it subsets a given font, it on;y subsets what that font is going to display. So for example, if you have ABCDEF the regular font will contain ABC and the bold font will contain DEF and the italic and bold italic will be removed because they have nothing to display.
Also, does glyphIgo handle ligatures? Some versions of ADE automatically use ligatures when you have the two characters together that make up the ligature such as fi or ff.
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