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@Firedancer885,
These epubs were originally downloaded directly from TTH. You can tell because a) they have the "Downloaded From: http://www.tthfanfic.org/Story-XXXX" line at the beginning of the first chapter and b) FFDL didn't even support TTH until 2011-12-14. Which is after the last update date for all of them as well. So I don't think FFDL has ever downloaded chapters for these epubs.
Looking back through the change history, I'm not finding anything in FFDL to explain this. I can't categorically state FFDL didn't rearrange the chapters, but I'm not finding any evidence that might have, either.
Regardless, it doesn't do it now.
Unfortunately, I don't see any easy way to identify books with this problem. And the only solution I see is to update with 'Overwrite Always' or download the epub from TTH again.
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