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I'm quite new to this game, having just bought my Kobo Touch this afternoon, however I've experienced the same problem, namely that my books don't seem to be available after they've been sent to the reader by Calibre. BTW, this is also based on placement in the main memory, as I am not (as yet) using an SD card.
There does seem to be a quick solution, though. First, the problem seems to be that Calibre groups the books by author, and places each author in a separate directory.
However, it appears that the Touch doesn't understand a directory structure (odd, wouldn't you think). I found that if I moved the books out of the subordinate author directories, and placed them up one level in the structure, then the Touch recognized them right away. It went through its "Processing content" dance, and after that I could read all the books, and see them in the Library.
This has the unfortunate effect of making somewhat of a mess of the Kobo's storage structure, but at least it makes the books available. I don't know whether to consider this as a problem that should be rectified by the Kobo developers, or whether it's a Calibre issue. It could be that the Calibre support files (metadata.calibre and driveinfo.calibre) are not compatible with the new Touch software, so that the issue is that Calibre needs to catch up.
My inflated $0.02.
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