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The book was incorrectly converted when the epub was created. Basically epub requires UTF-8. Odds are that was assumed/configured as the encoding when the original conversion to epub happened. Now that it's epub it's incorrectly encoded.
Your options are to manually fix with a series of search and replace - the ? mark characters are actually other strings that you could potentially search for and replace.
The other option is to guess the original encoding and try to re-convert. Under look and feel in the conversion options there is a box to set the encoding. cp1252 is a popular encoding, so you could try that, but it could be any number of things.
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