When you copied the new book onto the device, did you delete the old book first?
If you change the file structure by splitting up a big html file into one file per chapter and then transfer the book without first deleting the old book (using the remove function on the device itself), then the device will try to navigate the new book using information about the old book's structure, which can result in all sorts of strange problems.
If that sounds like the problem, you should be able to fix it just by deleting the book using the remove function on the device, then plugging it in and transfering a new copy.
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