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I used my "Quick and Dirty ePub Tutorial" 32-page pdf (see my signature) for testing.
I cropped headers and footers and then loaded the cropped file in BookDesigner.
The only anomaly was that the text "Page 1 of 32" (footer of the first page of the original file but not present in the cropped file) appeared at the top of the imported file in BD.
So it seems that the cropped off information is stored in the output file somehow, at least in part.
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