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It's likely there's a difference in how we generate our Kobo markup. I'm working on some changes, but with life the way it is for me I can't promise how long that'll take. In the meantime I'd suggest using Kepubify on the large files. If you save them with the .kepub extension you can import them into calibre as KePub format, and if you use the extended driver and set kepub as a higher priority format it's smart enough to not attempt to convert a KePub file again.
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