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FWIW I detest PDF on my reader and try to avoid that format wherever possible. Where I can't avoid it, I usually convert the pdf to text and then undertake the rather laborious process of creating decent html to convert the book to epub in Calibre. (I should add a disclaimer here - there's probably better ways to overcome PDF limitations - I'm still finding my feet in the area of ebook conversion. At least this way gives me complete control over little things like accented letters, emphasis, quote marks etc. Did I mention "anal retentive" anywhere?....). Hand-crafting in a text editor will also enable you to get rid of unprintable characters like your blank box.
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