Calibre/SD card issue - HELP!

[CS]

I used Calibre last night to copy my SD card books/samples to my PC, but now the SD card isn't showing any of those old books. They didn't get erased though, because they're still clearly on the card. However, I can't get the Kindle to recognize them (in fact, it thinks I have tons of space - and so does Calibre, even though that still lists all of the books that are/were on the card).

Now the SD card only recognizes new stuff I put on it with the Kindle.

Even more troubling, when I connect my Kindle to USB, the SD card no longer shows up on my PC. Before, I would get two "drives" after hooking up my Kindle via USB - the Kindle itself and the SD card. Now, I no longer get the SD card.  

(My PC has an SD card reader, so I can still access it that way, but it's not nearly as convenient.) (Edit: This part has fixed itself, thank God.)

What can I do?

UPDATE: I think I figured out what happened. That Calibre process somehow corrupted most of the files on my card. Grrrrrrrrrrrrr! It'll be a minor pain getting everything back, but it's not the end of the world. The only thing I'll lose are older issues of magazines, which I knew I couldn't keep forever anyway and rarely ever re-read, so that's not a major catastrophe for me. In a way, I'm glad to be free of all the old samples I had.