In klibrary, under markup/root, you will find folders (one for each 'book'). The annotations are stored inside those.
I have two methods for backup. One, I just keep a backup copy of the entire 'Reader' folder. I have tested it and, if things go wrong, copying the backup over the existing Reader folder will restore annotations (on your PC. You can then transfer that over to the device).
The second option is to use an SD card. Put it in the device and copy a book over. That will format the card. Now, you can put that SD card into any card-reader connected to your PC. Just drag and drop everything (through the Reader software) over to the SD card. That will create a backup copy of everything, including your annotations.
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