1) Make sure you disconnect properly, eject the device from Kobo Desktop, calibre, Adobe Digital Editions etc., before you pull the usb cable and waiting a extra few seconds after ejecting is probably a good thing to do as well.
2) Don't move from one software application to another without ejecting your Kobo first. As in don't download a book or sync using the Desktop software and then go into another software application like calibre etc., without completely disconnecting your Kobo first. You will of course have to reconnect to use the next application.
I have had four forced factory resets and I believe the last was due to problem 2 above. Since the last reset I have reloaded several hundred books without a problem. It's only a week but I'm feeling lucky.