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What are you exactly doing? How can you ask us if you are doing it right if you don't describe what you do?
As a rule of thumb, each chapter gets its own file. For a book of that size, I think around 12 chapters? So, including cover page, titlepage, colofon, dedication, things like that, you end up probably with a file of 20. You know you can split in one go? Use S&R, potentially RegEx, to identify the place of splits and insert a split marker. Press F6 and the split is executed.
Folders are not supported, at least not in this version. Perhaps in the next version this is possible. Some posts from KevinH seem to indicate that.
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