For annotations, you can try looking in:
/User/<username>/Library/Application Support/Sony Corporation/ReaderDesktop
/User/<username>/Library/Preferences/Sony Corporation/ReaderDesktop
If you don't like using the terminal, go to the Finder and hold down the option key while clicking on the "Go" menu. This will reveal the hidden "Library" menu option.
Sorry about not giving a definitive answer, but I don't use the annotations feature.
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