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The Nook ePubs probably have DRM (encryption). There are 3rd party plugins for Calibre that strip DRM when you import an B&N (say) ebook. See Apprentice Alf's Blog for more info on DRM issues. Note that in the US, editing an ebook to fix errors is a fair use that very likely makes stripping DRM legal (for such personal fair uses).
Once DRM free, you might be able to use Calibre's ePub tweak option (right click on an ebook with ePub and select tweak). Or use a full editor editor like Sigil.
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