I recently tried the Sony Reader PC app for the first time. I really enjoy the simple interface and attractive reading screen (it's right up there with Nook for PC for me). Plus, I like that you can export your notes into an rtf file.
However, something has occurred that concerns me. I spent the day reading a sideloaded ePub in Sony Reader -- not one purchased from Sony. I made lots of notes and highlights.
When I opened the book the next day in Sony Reader, the comments and highlights were gone.
Anyone else experienced this issue? I don't think I did anything to the files or the program to change it. There was probably a reboot in there somewhere, and it simply misplaced my annotations.