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Whenever an ePub file is opened with Calibre's ebook viewer, a bookmark file is created inside that ePub. This file does not store user bookmarks, it is automatically used by the program to remember the last used location inside the book.
More precisely this bookmark file is called calibre_bookmarks.txt and is located in the META-INF folder, inside the said ePub book main directory.

I'd like to know if there is an easy way of getting rid of these bookmark files from inside Calibre, ideally from multiple ePubs at once (doing it manually for every single ebook wouldn't be very handy), effectively cleaning them and restoring their "newness".

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There's a plugin called Modify ePub which could remove Calibre bookmarks. But I haven't tried it myself.

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    Thank you, it was exactly what I needed. Interestingly enough, I already had this plugin installed, but I had not noticed the option to delete Calibre bookmarks! :) – Sekhemty Dec 30 '14 at 23:00
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There is another way to do this on Linux.

First, open a terminal and cd into the folder with your ePubs.

Next, type the following command: find . -name "*.epub" -exec zip -d '{}' 'META-INF/calibre_bookmarks.txt' \;

Then, all of the calibre_bookmarks.txt files inside all the ePubs in the current dir (recursively) will be deleted.

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