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The best way to do it is to convert each book to text and load them both in Notepad++. With Notepad++, you can download the compare plugin and that will show the differences.
Thing is, one copy could have a preface, about the author, other books the authro has written,a review snippet section, one could be ePub 3 and the other ePub 2 and the ePub 3 ToC would be counted, could be a preview of some other book in one and not the other. There's a number of reason for the word count difference.
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