[Kindle Paperwhite] Highlights missing

[groob]

Hello,
I've recently connected my paperwhite with Calibre 5.5 via usb to transfer some new book to the device.

After this, some of my highlights and bookmarks are gone.
I could very verify this for a specific book, others seems unaffected, that is, the annotations are still visible as they normally should.
I still have to find if this has happened for other books as well but I could confirm for a specific one (azw extension).

The thing is that the annotations seems to be still inside My Clippings.txt but not visible in the book.

Just to be clear I didn't change anything to this book while this last connection. I've sent mutiple books to kindle via usb but didn't touch the book mentioned here.

Any idea what's happened or how to solve this?

[davidfor]

The My Clippings.txt actually has little to do with what annotations are shown in the book. It is really just a log of the annotations you have made over time. Each time you make an annotation, it is added to the end of the My Clippings.txt file and never used again. The annotation you see when reading are stored elsewhere. As you add or remove the annotations, they are added and removed from that location

I'm not sure where the annotations are actually stored. My memory suggests a file with the extension .sbr alongside the book. But, a quick search doesn't find any prove. It might be in a database somewhere hidden from view.

Because of this, I believe the connection between the annotations and book can get lost if the file name of the book changes. If you resend the book with a different file name, then the device won't be able to connect the store annotations to the actual book. And if something in the book is changed, it's possible the annotations will still be there, but, cannot be displayed when reading. They might be in an annotations list (I assume the Kindle has one), but, not visible elsewhere.

Note: My actual Kindle experience is limited to playing with them in a shop. Everything else is based on comments here and the work done maintaining the Annotations plugin.

[groob]

Thanks for your time answering this question.

Would that be for example because of a change of some tags related to that book?
If I've changed the name or removed/added tags inside Calibre would that automatically update my kindle once connected and mark the book as "changed"?

[groob]

I've found the folder containing my book.
Inside there was my book and a subfolder with multiple files.

/Book Authors
|---- MyBookName.azw3
|---- MyBookName/
|-------- MyBookName.apnx
|-------- MyBookName_GIBBERISCH_.azw3f
|-------- MyBookName_GIBBERISH_.azw3r
|-------- MyBookName_GIBBERISH_.bad_file

Does anybody know how annotations and bookmarks are organized in this file structure and if/how I might retrieve them?


Also that last

.bad_file

extension is quite suspect

[jhowell]

Originally Posted by groob

Does anybody know how annotations and bookmarks are organized in this file structure and if/how I might retrieve them?

See this thread: azw3r highlight and note extraction info

[davidfor]

Originally Posted by jhowell

See this thread: azw3r highlight and note extraction info

That would be a better way to extract the annotations than using the clipping file. Except that you would need to search for all the individual files and open them to see if they have annotations.

[davidfor]

Originally Posted by groob

Thanks for your time answering this question.

Would that be for example because of a change of some tags related to that book?
If I've changed the name or removed/added tags inside Calibre would that automatically update my kindle once connected and mark the book as "changed"?

The file name on the device uses the save template in the driver for the device. The defaults usually use the author and title. If you change these, and send the book again, it will probably put the books in different locations. That will usually mean two copies of the book on the device. What happens then depends on the device. If you have changed the save template, changing anything used in the save template will change the file name on the device.

[Frankee]

Originally Posted by groob

Hello,
I've recently connected my paperwhite with Calibre 5.5 via usb to transfer some new book to the device.

After this, some of my highlights and bookmarks are gone.
I could very verify this for a specific book, others seems unaffected, that is, the annotations are still visible as they normally should.
I still have to find if this has happened for other books as well but I could confirm for a specific one (azw extension).

The thing is that the annotations seems to be still inside My Clippings.txt but not visible in the book.

Just to be clear I didn't change anything to this book while this last connection. I've sent mutiple books to kindle via usb but didn't touch the book mentioned here.

Any idea what's happened or how to solve this?

Same here! Exactly the same problem. And it's not the first time.
It's so frustrating that after you plug your Kindle and open Calibre only to upload a book you could lose all the highlights and reading progress to.
I was at 88% of the book and I lose everything...

Any idea?