I'd guess that the books in your account are just links to the master file. I'm assuming that when Amazon sends a book to your Kindle it retrieves the master copy, applies the DRM, which attaches your Kindle PID to that copy of the file, and then sends it out. That way they don't have to store thousands of individual files tied to specific Kindle PIDs.
That's probably completely inaccurate but I'd bet it's something like that.
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