From nookDevs

Part of the NookColor portal

There are conflicting reports on whether it's safe to let a rooted NC install the 1.1.0 update. (I have a NC rooted using Nooter, and it seemed to work just fine, but IRC reports issues on other nooks.) Best to be careful and paranoid until more testing has been done.

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As of February 5th, there is a new Auto-nooter 3.0.0 that will Nooter (Root) only Nook Colors running 1.1.0. (Note the ONLY) This process is similar to previous versions of Auto-nooter, so please read the instructions completely before attempting it. Here are the instructions and XDA Forum thread. If you have rooted your device already and used the CWM 1.1.0 updater as listed below, you should be good to go.

Note: If you have rooted your Nook Color but want to start over, I highly recommend Flashing to Stock following this XDA thread by using Clockwork Recovery and their image of a Stock 1.0.1 ROM. Then registering your device, update the NC with B&N's sideload of 1.1.0, and then using Auto-nooter 3.0.0 to root it. At this point, use a prepared-bootable Clockwork MicroSD and Backup the ROM in this initially rooted state. This will make restoring to this point a breeze if you muck around with ROMs a lot.

As always, read instructions wholly and completely before attempting. Though I've done an incredible amount of emotional damage to my Nook Color, I've never bricked it, but your results may vary. :)

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If you already have a rooted 1.0.1 and you're using clockwork recovery, there's a pre-rooted "update" image for 1.1.0 in this XDA thread This seems to be working fine for some folks, but with a variety of issues for other (some of which have workarounds posted in the thread). It's not fool-proof yet so read the thread carefully.

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There are two other alternates, for use with 1.0.1 or stock 1.1.0:

- Flash with Clockwork Recovery from an SDcard, details here

- Use "unofficial" update to Auto-nooter 2.12.25, details here

Both these methods are subject to the warnings above.