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I've been using calibre since 6.41 and I've never had it mislay even a single ebook out of the 2500 or so I have in my library, so I can't agree with you that it "easily" loses books.
If you're mucking around in calibre's private library files, this may have something to do with your vanishing books issue. Don't try to "clean it up"; just let it alone (read my .sig).
As for the proper place for bug reports, that's kind of complicated. If it's something that may be a user issue -- that is, if you've broken something -- you can usually get help/answers here. However, if it's a genuine calibre bug, you need to open a ticket with the bug tracker so it can get fixed.
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