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I have used calibre since I bought my Kobo in July and have never had a problem with the database because of it. It is a simple program to manage epubs and a pleasure to use.
If you do have problems with the database (and my wife has had a kobo as long as me and never has had a problem and mine were really my fault for trying to tweak where I shouldn't have been and a problem with an old desktop app which has since been updated) the new Kobos let you restore it to the original settings quite simply through the menu.
Welcome to Mobile reads!
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