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Make sure calibre is transferring AZW3 files to your Kindle. (MOBI file format can't include fonts.) I suggest changing the metadata on the version in which you've embedded the font.
Ummm... do remember that just changing the font which calibre uses to display an ebook won't actually change the ebook. Embedding the font will require individual editing of the books, unless there's a plugin that does it.
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