on the device,
if rooted you can access
notes and apparently svg-drawings? here:
/mnt/sdcard/Sony_Reader/media/notepads/
also some SQlite .db files here:
/mnt/sdcard/Sony_Reader/database/
external microSD holds sqlite databases as well, access on reader::
/mnt/extsd/Sony_Reader/database/notepads.db
I can:t find it right now, but i think i saw once that my marked up text and annotations went somewhere into those .dbs.
EDIT found it:
see mobileread wiki, and this
firefox addon really is pretty good.
I did search for your library file but couldn't find any.