Yep, that's what happened. I expected that they'd show up as Purchased rather than with the books I didn't get from Sony, but they're now there. Thank you all so much for helping me recover these. Sony still doesn't get off the hook for being so unhelpful, but you guys are great!
The only books which show up in that folder under Documents are the ones in .lrf format, and excludes all books in other formats. I still haven't found where those hide for backup purposes.
