Thanks everyone for the feedback. I'm using Mercurial, and unfortunately the eol support is rather screwy.
It's easy to make a case either way: that LyX should produce consistent output, or that LyX is not responsible for line endings. I'm having problems because of inconsistency, which I feel is at least partially LyX's fault. I agree with Abdel's points--I'd personally be delighted with mandatory LF output. Notepad already fails so often due to LFs that few consider it a viable tool for file editing. A thread on StackOverflow recommends effectively replacing output.WriteLine(foo); with output.Write(foo); output.Write(LineTerminator); Of course I defer to the experts on whether LyX should take control of eols, but I have my hopes. :) -Ben