UPDATE: after more thought & more googling. I am pretty sure that sony reader for PC software also keeps a copy of books.db - see the link below for location.
so if you are using this software it may be synching with your T2. T3 and keeping a corrupt version of books.db in circulation
I don't "read" within that software, I only use it to authorise library book loads, so others may know more about how it syncs than I do. Logically it needs to do some sort of merge/update to preserve notes etc on both PC & device.
( I don't have the software active when my T3 is connected, I move books from reader folder into calibre & sideload from there to my device. )
if you don't use the PC software then ignore this hypothesis>
http://www.sonyreaderboards.com/foru...&t=52&start=10