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Sounds like you should create an input plugin that walks the contents of the epubs zip file and adds any files present but not manifested that are css, image, font, or xhtml files to the manifest, and the xhtml files to the end of the spine in a some pattern (but what order?). You might want to include unmanifested javascript files as well.
It appears that these bad "epubs" are nothing more than a zip of a website that has been scraped.
Alternatively, unzip these "books" first and then use Sigil's Add Existing ... menu to pull in the pieces you want.
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