You need to start your book over again. You need to set Book Designer for German and then reload the book. Do not use the html0 file if you have one. If you have the Book Cleaner 1.5 files in place and set right with 1 being the input and 2 being the output, then you should be good to go.
But one thing to do is check the original source to see if there are em dashes or double dashes. If not, you won't have any em dashes.