I encounter the same problem as explained in this blog, when I print a pdf from evince hyphens are not printed. when I print a pdf from Okular, hyphens are printed. For example the hyphen that appears at the end of the first line in this text:
Both evince and Okular are recommended pdf viewers on the Debian wiki, but I would prefer to use evince since it's the default for Gnome and it's already integrated with some other software I use.
Here are the Latex and Lyx files that can be used to generate the problematic pdf: hyphen.lyx