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If the next update is anything like previous ones - it will break root (which will disable applications that require root access to work) but it shouldn't disable any other applications that are already installed - such as Kindle or the Android Market.
There's no guarantee - but once you've got the Kindle App on there, you should be able to continue to use it. Also, because the methods being used to root the NC are based on hardware rather than software, they are unlikely to be able to lock people out permanently without changing the hardware. The NC2 may not be so easily rooted, but that won't affect existing Nooks.
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