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Hi, Kovid. Thank you for your response.
I was already removing the annotations from those 3 places, but they kept being restored.
And I have just found out the 4th place where JSON files with the annotations were being stored: ~/Library/Preferences/calibre/viewer/annots.
(I forgot to mention in my original post that I am on macOS).
By deleting those files, in addition to the database records and the book's OPF file, and then syncing the highlights again, it works now: the E-book Viewer is no longer restoring the old state and it's displaying all the highlights!
Out of curiosity, may I ask what is the purpose of keeping the annotations in this folder as well, in addition to the 3 other places?
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