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Hmmm...
My epub to epub conversions always look the same after converting unless I explicitly want them otherwise.
I just checked a few to be sure. I have done a few thousand and not noted any peculiar results. Same margins, same text at top of page 100, pictures ok if there are any.
Perhaps you have setting set wrong somewhere in preferences?
I believe you can use sigil as they are epubs and type in the metadata yourself.
Or cut and paste from calibre.
Best of luck
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