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Comparing two files of the same format is used to determine what edits have been made between two versions of the same book.
It isn't practical to compare different formats because there are major differences dictated by the constraints of each format. For example, AZW3 does not preserve internal file names so it is likely that none of the files that make up the content will match up with the same book in EPUB format.
You could convert from one format to another so both files are in the same format for comparison, but this conversion will itself introduce new differences.
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