Originally Posted by katb
I had the same problem with my reader software till I came across this solution - it worked a treat for me
I opened my Sony Reader Library software without my eReader connected. In the left-side panel, I clicked "Books" under "Library" so that the books I've imported showed in the right-side panel. This next part might take a while if you have a lot of books -- I double clicked each book I have to preview them (or right-clicked and clicked preview), until I came to a book the software couldn't find. I deleted that book, re-connected my eReader, and everything synced up just fine. Afterward, I re-added the book I deleted and synced again. I haven't had a problem since.
There were about a dozen books on mine that were missing - but totally solved the problem - hope this helps
Thak you so much! After hours of flailing, this worked like a charm.
One note: I did discover that one doesn't need to doubleclick on each book--if one doubleclicks on the first one, one can then use the arrow at the top to go from book to book, quickly finding the bad ones.