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Apologies in advance for the vagueness to follow: I mostly use Modify ePub with 3 options checked (Remove Unused Image Files, Insert or Replace Cover, and Update Metadata). After Modify ePub finishes, I use Open With Sigil to check for other stuff I may want to fix. Occasionally, after running Modify ePub, when I open the book with Sigil all of the .html files have been rearranged in alphabetical order, which means "Epilogue" displays before "Preface", etc. I thought this might be a Sigil problem, but if I start from scratch with the original epub and use Calibre's "convert epub to epub" function, it doesn't seem to occur (nor does it occur if I run Modify ePub AFTER I run Calibre's conversion). I also tried using just one Modify ePub function at a time, and it doesn't occur. So I guess my questions are: 1) has anyone else seen this behavior (which I cannot duplicate reliably and which seems to occur randomly), and 2) do you think this is a problem with Sigil or with Modify ePub and how on earth can I track this down?
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