elminster, thank you so much!
The Sony software somehow deleted lots of my books and notes, and I managed to find the .annot files still hidden on the reader, the same place you found them I think. But I couldn't get them to work again with the same re-downloaded books no matter what. I started a thread here but no help on that front and I scoured google with no help on .annot files either. Then as a last resort over a week later I thought of searching mobileread for .annot and see what comes up, and of only about a measly 20 results from the entire site, how lucky was I to find this one with the solution to the exact problem I'm having!
Though it took me awhile to get it right since what you were saying almost looked like a foreign language at first (I'm very non-tech), with patience I succeeded and I'm so appreciative that now all my hundreds/thousands of notes aren't gone with the wind. Thanks!