Device updates that break root are fairly common - in fact, I'd go so far as to say that the majority of updates do so. What's a bit less common, though, is an update that resets your device because you're rooted. The device in question here is the NOOKcolor, and unfortunately it looks like that's exactly what's happening.
Before I dive into the details, I think it's important to note that I doubt that even as much as manufacturers and carriers dislike when people root their device, it's pretty far over the line for them to remotely wipe the devices of people who have done so. In other words (TL;DR), I think it's unintentional and B&N has no nefarious intent.
Thanks to some detective work by leeh41, it looks like the issue is that there's an update rolling out for the NC, but some rooted users are running an auto config script that disables OTA updates. When the NC tries to ping the mother ship for updates, it results in an authentication error, and because of this, the device thinks there's some sort of glitch in the software and does a full factory reset. At this point in time, it looks like the fix is to manually remove the relevant code from the script, as shown in leeh41's post - but then you're open to OTA updates.