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Annotations are stored in SQLite database /data/data/com.bn.nook.reader.activities/databases/annotations.db
To access them from the rooted nook, copy this file onto your computer (using adb or some file syncing app), and see the table with some SqLite db browser program (for example, SqLite Manager plugin for firefox browser).
There are also SQLite apps for android, like 'SQLite Manager', you can try using those to see it on the nook directly.
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