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Update: I found that by deleting all the books from my device, deleting all the metadata.opf files in my collection and re-uploading all my books, all my books are now showing as having no Category in iBooks as expected. I think a change to iBooks, Calibre or maybe both must have happened in the past 6 months as books that were previously "Uncategorized" now have no category at all.
So if metadata's got you down, try cleaning it with Sigil first, but if that fails delete the metadata.opf files and you should be able to scrub your books clean.
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