Originally Posted by davidfor
You could extract the annotations from the database and insert them into the current database. But, I have tried this in the past and it didn't. My tests show that, the annotations file takes precedence. Whatever is in that file will be read when opening the book.
, I still think there is some hope. Maybe that the annotations file takes precedence over the database entries as said by Davidfor, I did not make any test in this respect. Anyway, I would suggest that if the annotation files do not bring the annotations back, then delete those annotation files and the manifest files (not sure whether deleting the manifest files is necessary, but does not hurt), and copy the bookmarks of the epubs (but not of those of the kepubs bought from Kobo) from your old database to the new database. If there are is not an annotation and manifest file for an epub on the device they get reconstructed from the database entries. By the way, in the case of kepub.epubs (maybe you have some of those too) the database is the only place where annotations and highlights are saved.