Thanks for the reply bridgetostars
Well, now I think that I sorta
know where the annots are. Somewhere in the (hidden) "data" partition. See here - http://robotskirts.com/media/text/nookfslist.txt
(it's a file listing from a rooted nook). I've tried a couple of things to try to mount the hidden ext3 partition but access is disabled by default (or so I deduced at least). When you softroot, you can use adb to access it.
I'm positive that digging through the files on there will easily uncover the annots. *sigh* I guess I'll wait for the upcoming update, see if it resolves the annotation problems. If not, it's time for a softroot and a headfirst dive into those beautiful looking files on the "data" partition