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Well, they can tell what you do with it within the application itself -- that's how it's going to be able to sync pages between the desktop and Kindle versions.
If you're asking if they can figure out if you strip the DRM on a file, assuming we can ever figure out the PID, I would say no, unless you re-import the de-DRM'd version back into the application.
If you're asking if they can track the file if you rename it and copy it to a different directory and never open it in the Kindle app, then I would say no, not absent some kind of included spyware. And if Amazon did that, it would make the Orwell thing look like a cakewalk by comparison when they are caught.
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