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To prevent the epub reader creating a second persistent copy of annotations for books in internal storage:
1. Go to the Digital Editions directory on the device and delete the Annotations subdirectory and everything in it (back up first if you are not sure.)
2. Create a normal file named Annotations in the same place as the deleted directory.
Thereafter epub annotations will still be saved in the database, but the epub reader will not be able to create the file in Digital Editions/Annotations/ containing the second persistent copy.
This also fixes the issue of the annotation chapter and location info being corrupted when an epub book is reopened. (It doesn't fix annotations that are already corrupted, but it will prevent future anotations from being corrupted).
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