Since you have not been using Book Cleaner, it could very well be that your LRF editions have had the em dashes convert to plain old dashes.
That said, there's a thread on Book Cleaner on setting it up and the configuration files to use. I started this since I don't really like it when em dashes get converted to dashes.
https://www.mobileread.com/forums/showthread.php?t=11649
One other bit of info... when using Book Designer, do not load in text files. It seems it has a bug where it can and sometimes does split paragraphs. Convert the text file to RTF and then load it and that won't be an issue. HTML is also not an issue.