I'm, guessing, from the lack of replies, that not too many people have had this happen to them.
I did find a thread in this forum by someone who had a similar experience:
https://www.mobileread.com/forums/sho...d.php?t=120302
Unfortunately, it seems the cause was never determined and there isn't any information in the thread I can make use of to fix the problem. Though from now on I am going to be sure to back up my reader folder.
The odd thing is, the poster describes having had this experience before the problem arose:
"Before this happened yesterday I was reading an e-book on my Reader (a book that was originally in eReader PDB format), and I noticed that when I got to chapter 3 the font was suddenly smaller. I looked at every other chapter in the book and verified that only chapter 3 had the smaller font. I thought this was strange. Then later in the day I noticed that the font size for chapter 3 had returned to normal. After that I went to my list of notes and realized that all of my annotations for chapters 1 and 2 had disappeared, and I only had my notes starting from the beginning of chapter 3, the spot I had noticed the mysterious and temporary change in font size."
I had the very same experience before I lost all of my notes. I was reading a book in which the font size mysteriously became smaller for one chapter. I can only conclude there is some kind of rare bug in the software somewhere that causes this.
Right now I am mainly concerned with trying to find some way to access the annotation files which did not get erased. (I came to realize I lost the ones I did because I opened those books in my reader and went to look for my notes--as soon as I did that, the Reader overwrote my old annotation file.) The rest of my annotation files are visible in their folders, when accessed from my computer. But the Sony Reader cannot seem to see or access them. I tried backing one up, and then creating a new notes file for the book, and then copying the information from the old annotation file into the new one, but this doesn't work. The Reader refuses to see any of my old annotation information and will not let me do anything but create an entirely new, and empty, annotation file.
Does anyone know what is preventing my Sony Reader from seeing the information in the annotation files which I can see are physically there on the disk? It seems like unless I can get it to see them, all of my annotations are lost. I have tried looking through the files for information, but there is nothing there I can understand. I can't find anything listed there like page numbers, which would allow me to at least refind and rehighlight the same passages.