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Originally Posted by redscarlett
I'll email it you now.
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The file names inside that epub have all been changed--the same way calibre's epub->epub convert changes them. file0001.xhtml becomes something like file0001_u12.xhtml.
I might have been able to adjust for the file renames, but the convert also throws away metadata files that FFDL (EpubMerge called by FFDL technically) needs to 'unmerge' the anthology epub before updating each book inside it.
Maybe you ran convert to embed the cover image, not realizing that it would change more than that--that used to be the recommended way to embed covers. Now, however, you can embed the cover image using either the Polish tool or the Modify Epub plugin. They don't break anthology update.
If you have an ORIGINAL_EPUB format in that book, you could restore it and then anthology update will probably work.