Here's what I do to add books from my Kindles to Calibre:
1 - plug in the Kindle and wait for Calibre to recognize it.
2 - choose the device icon next to library.
3 - highlight all the books I want to add.
4 - right click one of the books and choose "add to library".
5 - wait for it to finish adding the books.
I have 2 Kindles and I created 2 custom yes/no/undefined - one called Kindle DX and the other called Kindle WiFi. I mark the books I added as yes in the correct column and then I can always see the titles I have on each of my Kindles. I have saved searches so I can pull up only the DX or the WiFi.
Then I can create a catalog for each reader. Ya' gotta love Calibre.
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