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Originally Posted by Jellby
What I want is keeping only the annotation files that contain some actual annotations. If I need to backup the annotations or look at them in my computer, these files are useful. I haven't tried saving the annotations from the database yet, but the files are easily readable without calibre.
Cleaning up the annotation files would also let me quickly see which books have real annotations (by just seeing which files are there).
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That's a useful reason.
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1 and 4: No, although it could be used if you want to remove duplicate information. Or if that forces the device to re-generate the annotation files
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#1 will definitely be an option. That is because when you reopen the books, the file is reread and replaces the annotations in the database. When that is done, it screws up the chapter and percentage displayed in the annotations list.
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2, 3, 5: Yes. Those files would be pretty useless.
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#2 is interesting. When you delete a book using the device, it doesn't delete the annotations file. Hence if you delete the book, and put a new copy on, you get the (screwed up) annotations. Some people take advantage of this.
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This is all assuming that under normal conditions the database and the annotation files contain the same information. Have you seen that this is not the case? I had a quick look and the annotation files for the books which I know I have annotated do indeed contain at least some of the annotations, the files for books I have annotated and then removed the annotations are "empty", the files for books I have not annotated are "empty" too. It's these "empty" files i don't want there.
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Yes, that seems to be the case and I can see a reason for removing the clutter of the empty files.