The calibre command line program 'epub-fix' will change an epub to work around various bugs in epubcheck. The command's help text is:
Usage: epub-fix.exe [options] file.epub
Fix common problems in EPUB files that can cause them to be rejected by poorly designed publishing services.
By default, no fixing is done and messages are printed out for each error detected. Use the options to control which errors are automatically fixed.
Whenever you pass arguments to epub-fix.exe that have spaces in them, enclose the arguments in quotation marks.
--version show program's version number and exit
-h, --help show this help message and exit
--unmanifested Fix unmanifested files. epub-fix can either add them
to the manifest or delete them as specified by the
delete unmanifested option.
Delete unmanifested files instead of adding them to
--epubcheck Workarounds for bugs in the latest release of
epubcheck. epubcheck reports many things as errors
that are not actually errors. epub-fix will try to
detect these and replace them with constructs that
epubcheck likes. This may cause significant changes to
your epub, complain to the epubcheck project.
Created by Kovid Goyal <email@example.com>