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Thank you for the replies.
elcreative, I did have Calibre and Reader Library open once at the same time, but only because I did not yet know that Reader Library by default opens automatically when a Reader is connected! Live and learn, I guess. I closed Reader Library immediately and thought I'd be okay, but I suppose something could have been corrupted.
vxf, on my computer there is no markup/root in the klibrary folder, just two books for which annotations (highlights, notes, etc.; I haven't used the handwritten notes feature) do show up when I open them in Reader Library. I have my computer set to display hidden and system files, by the way. Are the annotations files supposed to have names ending in epub.annot like the ones on the reader? I can't find any such files at all on my computer.
Backing up the Reader folder sounds like a good idea. The PRS-350 doesn't have an SD card slot, but I suppose I could use any type of media to back up the library the way you describe. And I guess the location of annotations files may be a moot point if I can just drag and drop from the Reader Library to back everything up. I'll try that.
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