It is nothing to do with this plugin, since all it does is populate a custom column. This plugin has nothing to do with the actions of sending books externally
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I don't use email to my Kindle myself so I can only guess at the answer. I would guess that even if calibre were to attach an apnx file to its email, that Amazon strip it out. You could try it for yourself just by manually emailing your Kindle with an APNX file and see what shows up on your Kindle. If Kovid spots this through his heavy eyelids he might comment further, or else do a search of the forums, it is a question that has come up a few times.