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It was a document I downloaded from a forum. Not sure how it had been made, but possibly it was a converted scan of a pdf. It was only a short little thing - about 12 pages on my reader, so fortunately my solution while inelegant (and impractical for a full length book) was fine here. I just opened the document in Sigil and highlighted and typed over all the apostrophes and the letters either side, hopefully replacing whatever unrecognised symbol was hidden in there. I did notice that when I typed an apostrophe it looked slightly different to the ones I was replacing.
I then saved the document, put it back on my reader and all the squares were gone. Probably not the best solution but it got the job done. Not really the answer for a proper book-length epub though. Would have taken ages.
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