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If this is a concern of yours you might want to get Calibre. It is an ebook management system and library for your computer (Windows/Linux/Mac). One feature of it is that you can change metadata on your books and then 'republish' them as long as they don't have DRM. I haven't played around with margins, but this is supported in Calibre.
You could load all of your DRM-free books into Calibre, set new margins, and then tell it to 'convert' all of your books to update them with the new margins.
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