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Others will have more specific advice about getting rid of the duplicates on your device, but as a n00b who just got an T1 about 2 weeks ago, I recommend using the free Calibre software to manage your library and load books on and off your device. Calibre installs easily for Windows or Mac and, with the addition of some other tools, can make Kindle and other non-epub books compatible with your device. I turned off the automatic sync function in the Reader for Mac software so that it doesn't even launch when I connect the T1 to my laptop.
Bottom line is that this problem can be fixed and there is an easy and I daresay elegant workaround that's easy to get up and running.
I would offer suggestions for fixing the duplicates on your device, but I don't actually know how to do it. I didn't have the problem of duplication because I was fortunate to find out about Calibre before I got my device (shipping took over a week and I came across the info while reading all things T1-related while I waited to get the device in my hands). If you poke around here in the forums a bit, you will come across other threads that have discussed this problem specifically.
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