Well, clearly there was a part that I missed in my estimations. Registering a device with Barnes and Nobles always occurs prior to rooting, so de-registering a device will work in the rooted state, but you can't re-register it under a different name rooted.
Ended up having to start from scratch. Fortunately, the Autonooter 3.0 makes things go a lot faster these days. Unfortunately, B&N update 1.1.0 + Autonooter 3.0 yields strange wireless cut-outs coming out of sleep that I've never had problems with on previous B&N updates.
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