I haven't played around with multiple libraries yet, I will give it a try soon*
The thought crossed my mind as well that the 'update only in list' idea would also be nice in a scenario with a list of favorite fanfics. That way favorite stories that have been read and removed from the device can be automatically placed in a send to list when an update rolls along.
In an ideal world, I would like to have all my fics on my nook, but the default library is... lacking, and makes it inconvenient to have a large number on at a time. I looked into alternate libraries a while ago, but none seemed to work nice on the thing.