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It's a problem that plagues all of us at one point or another.
Fixing it can be difficult, depending on formats and tools available, and time-consuming.
I often use Calibre to convert books from one format to another, with decidedly mixed results.
If I can get away with it, I prefer my book in rich text format (.rtf), which I can then open with a simple text editor like gedit (I use it in Linux; it is a bit more powerful than Microsoft's Notepad) and do search and replace routines.
Calibre does have some of this functionality built-in, I believe, but frankly I use it only as a conversion tool and am not versed with all of its functionality.
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