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Looking at that log, about 30,000 files ended up being copied.
I am guessing that the epub reprocessing did result in many files being changed looking at the elapsed time that it took. In the 2.5 beta 1 version the statistics written to the log have been extended and would have told you how many files were re-processed so you could be more certain. Note that files get re-processed if the .opf file in the book's folder is later than the epub file. Did you perhaps tell Calibre to do a backup as that would update all the .opf files?
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