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Calibre should be able to do what you need, I just looked in the conversion stuff and you can set margins (all of them) when converting. The option is under "Page Setup" in the conversion dialog. You'd just need to create a custom output profile with the right margin set much higher than normal. Since you can run a conversion to the same format the book's already in, this would work great.
As AlexBell mentions, you'd have to deal with DRM first (if the books are DRM'd), but past that Calibre should handle everything and make it a lot simpler. Once you have the profile settings figured out, you can reuse it over and over again.
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