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Duh!
After hitting myself on the head for not doing the obvious, I set the preferences and the next file (a news section from the Christian Science Monitor) transferred into the right directory. For some reason, however, the ePub version was the one that transferred. Both versions, the one I converted and the original ePub, are in the Calibre directory on the computer.
Once I figure out all the intricacies, I'm going to love this program.
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