Occasionally, the Reader (or is it the software?) will "belch" [F**k up], regardless of whether the sync feature is on or not. I use the sync feature, but many people don't like it.
Whenever something happens, I delete the everything on the Reader this way: Plug it in and delete every folder on the Reader. I then unplug it and let it go through the process of loading nothing, which takes about 1 second.

However, keep in mind that everything currently
IN the Sony Folder (on the computer) is exactly what is on the Reader. When something is read and deleted from the Reader, I also move it
OUT of the Sony folder and put the file into a
Books Read folder.
Now, if the sync feature is on, just plug the Reader back in and load up the Sony software. Every book that was in your library (in your Sony Library) will be synced back to the way you had it, along with your collections. Bookmarks will be lost.
I've had to do this about three times total, probably because I carry about 300-350 titles (mainly novels) on my Reader. I only have about 7 megs left on the Reader. Whenever I finish reading something, I delete it.
One time, I had about 10 megs left, and wanted to load some newer titles onto the Reader, but it stated I didn't have enough memory. I suspect the memory on the Reader had
BECOME FRAGMENTED and would not allow me to load even one title onto the Reader.
I then deleted everything, using the process I just described. (As a safety measure, I copied the folder of books on the Reader onto my computer - even though the books were already in the Sony's folder on my computer. This was just a safety precaution.)
Then, with everything deleted on the Reader, I did a sync and everything in the Sony folder was synced back onto my Reader, and then everything was fine. So, the memory
can get fragmented, just like on a hard drive. After all, it
is a drive, and deleting and adding can compromise performance.
Don