If your Nook or Nook Color device goes missing, you’ll need to call customer service at 1-800-843-2665 or de-register your Nook at bn.com. The company says that you are liable for all purchases made until you de-register the device. You should also change your bn.com login credentials immediately.
One of the benefits of a Nook ereader is that all side-loaded content (i.e. all of the potentially sensitive documents you uploaded to your Nook yourself) will be safe as soon as you de-register the device. However, you will not be able to retrieve those documents.
Should you decide to replace your ereader, you will be able to redownload all of your content once you sync your new device with your bn.com account.