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Calibre now has a built in ebook editor for epub books. You can convert to epub and then edit as you please, including using search, search-and-replace and regular expressions. Afterwards you can convert to a suitable format for your device.
But you would most likely benefit from starting with some format other than PDF. PDF is most likely the worst possible format to download if you intend to convert to another format. It is even possible that the problem goes away if you start with some other format.
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