This is likely due to the encoding of your lit files using "smart" quotation that looks nice,but doesn't convert nice. You can try and change the encoding on the conversion options from autodetect to several other encodings (try searching encodings in this forum for several threads on different encoding types to try), but many of us have found that this doesn't work and requires you to manually change the quotes, em-dashes, commas, and apostrophes to non-smart quotation marks.
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