For future reference if you have enough to manually edit when you do a find/replace like I mentioned and select all text files it looks through the entire book, so you only have to do it once per book
Your method works well if you're replacing the epub but I'm not sure if it'll screw up Fanficfare future downloads. Not at home to check that. It also is a lot faster for multiple files, but be careful about just removing <br> because depending on how the books setup internally you could get one solid paragraph.
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