Thanks very much for the explanation on where Calibre sends the files and about the difference in the way Aldiko and Moon store files. I am still trying to figure out exactly where files are being stored on the Nook. I started using Calibre on the internal storage card so some of the books on the internal card may be from that time. The Nook part of the OS simply lists files as "Books" or "Files" and it doesn't seem to matter which card they are stored on. They all seem to be listed under "Books". There is a separate folder for Calibre Companion.
When I get this straightened out for sure I will post an update.
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