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In Calibre go to Preferences then in the "Conversions" section click on "Common Options".
In the "Common Options" window make sure you are on the "Look and Feel" section and then, at the bottom, click on the "Filter Style Information" tab.
In that tab check the check-boxes according to what you want removed (Margins is one of them).
Then convert from EPUB to EPUB and this should work OK.
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