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Edit: I found some interessting method to get rid of all epub errors. At least the one which are shown by the internal calibre bugchecker. Maybe somebody can confirm if this is also working for epubcheck as well, because as mentioned in this thread, epubcheck finds more bugs than the internal bugcheck. So all I do is this:
Select around 50 ebooks already in epub format (with various bugs), convert them from epub to mobi, delete all epub formats, convert them back from mobi to epub, delete all mobi formats and there will be no more bugs found in the internal bugcheck scan. I read somewhere here that it could help to convert epub to epub again, but there were still some bugs in the scan afterwards. With this method I see none. This method takes less than two minutes for 50 books (depending on your pc power of course). So let me know if this fixes most of the errors in epubcheck as well. That would be great. Thanks again
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