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It sounds perhaps like you should have done some more reading before jumping ahead to Froyo installation. When you install Froyo, you are installing a whole new operating system...not just upgrading the stock Eclair. It is as if you were to install Linux on a computer that used to run Windows...you will not have access to anything that was on the old system as you have replaced the operating system. The Nook software that was present on the stock Eclair will also not be there, and for some reason the Android Nook app does not yet work on Nookie Froyo, so you will not be able to access your B&N books.
If you installed Nookie Froyo to SD card and are running it from there then the fix is quite simple....take out your SD card and reboot your Nook. It will boot back into your rooted stock Eclair and all will be good. If you installed Froyo into your internal memory, then you have overwritten your old OS and cannot recover it. You can get back to a version of the rooted stock Eclair, but it will not be YOUR version with your old programs. Directions on how to get back to rooted Eclair are in this thread:
If the Market still thinks that you have apps installed that are not on your device at that point, then I don't know how to help. Perhaps you can try and get some help from Google...explain that your device failed and you had to get a new one and now you can't get your apps back.