Quote:
Originally Posted by theducks
 (not tested, a bit tedious)
Since annotations is a simple text file (clippings.txt), copy that to a WORK AREA on your PC (a backup).
Now add your new book version: Make a simple annotation in the new book (causes a new note to be added to clippings.txt): find that with a text editor (notepad), Add your old BOOKS notes (merge) into that. USE CARE TO NOT MODIFY THE STRUCTURE OF CLIPPINGS. (you do have a backup)
Make note to self: 'don't change titles AFTER making notes in that book 
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While that will work to update the My Clippings.txt file, it does not make the annotations available when reading the book. The My Clippings.txt file, is really just a log of any annotation and highlights made. Doing this will allow the Annotations plugin and other tools that read the file to get them. But, it isn't used by the device to display annotations when reading.