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I don't think that mobi can not save series information in the book. Someone else might correct me, but that explains your symptoms.
If you are saving a format that cannot hold series information, then you must save the opf file along with the book. Calibre will use that file to get the latest series information. Same thing with cover -- if for some reason calibre cannot save the cover in the format in a way that it can later identify as the cover, then the only choice is to save the cover separately.
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