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I putzed around with this issue also and for me it was just easier to uninstall Aldiko and delete the ebooks folder, then reinstall Aldiko.
Aldiko needs a better library management system in my opinion. When you get to a large number of books (probably larger than most people would have) the import gets extremely, extremely slow. A live search (like the Nook's default library search) would be nice as well.
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