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@Sidetrack - if it has been asked for before then it was a long time ago, then again I do have goldfish memory and been a long time since I updated this plugin. It's an interesting idea, I will have a think about it the next time I look at this plugin.
@LadyKate - a binary search is an *exact* match type search on the underlying files, so yes bookmarks screw things up. Personally I turned off calibre bookmarks a long, long time ago because (a) I don't read books using the calibre viewer, and (b) I was getting annoyed with the contents and timestamps changing every time I opened one up to look at it.
All I can suggest is turning off the feature (in the Preferences in the calibre ebook viewer application itself), and then using the Quality Check and Modify ePub plugins to find ePubs with Bookmarks and remove the bookmarks respectively.
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