For newbyes newbyer than me only: I have experienced some troubles when going from LyX1.1.5/PC-winNT to LyX1.0.4/Unix with protected separators. When opening the file in the unix system, I get InsertSpecialChar errors ~. One easy solution is to use a text editor and query/replace the string \SpecialChar ~ by the string \protected_separator Hope this can help.