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You can find some epub2 ebooks with the same structure and they are also not happy campers when splitting omnibuses.
From either a downloaded ePub or using KindleUnpack to generate the epubs to avoid the calibre artifacts, Vellum created ebooks are not a pretty sight. I run into quite a few from my spouse's ebooks. After the first few, I ended up with a set of saved searches in Sigil to clean them up which then allows splitting omnibuses with a lot fewer issues.
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