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First of all, what do you mean by "rooted"? Rooting just gives you access to the operating system. And then there's changing the ROM - replacing the B&N version of Android with CyanogenMod or other version of Android (you have to "root" it to be able to do this).
If it's just rooted, you can deregister it through the settings and register it to yourself normally (I've never messed with deregistering - B&N can help you do this).
If the ROM's been replaced, you can just download the Nook app from the Google market and register it under your name. Your content should then download to your Nook. If you're wanting to restore it back to the original B&N Android, then do a search on xda-developers.com (or Google) for instructions on how to do this.
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