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If you are doing any reformatting of the text, you may find it easier to do so before you split the file.
This only really works if the entire book is formatted the same. If it is a collection of previously formatted books (all formatted differently), then it is easier to split first.
You can generally tell by the number of css files. If there is one, then the whole book usually formatted the same. If there is one per sub-book, then they are generally formatted differently.
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