It seems to me that the traditional "\n" does not work with the FLfile.write method properly.
I was working on a little extension, and I would be passing String data up from a SWF using MMExecute(). IN JSFL, when i did a few alert or traces to check the string, eveything seemed fine, but when written to disk, all line breaks were removed.
For this extenion it was crucial that I have the line breaks, so I had to keep trying to figure out the issue. I determined that 100% FLFile was stripping them out. If i write the string to a file using the fl.ouputPanel.save(), they were in there.
So at the end of the day I just ended up doing a character code output and comparing the edifference between a file that was properly written vs one that was stripped. The difference was the missing char 10.
So instead of using newline(in AS) or \n in my string generation, I used this instead String.fromCharCode(13,10). Pretty simple, but it is annoying when documented examples of using this functionality fail, making you search through your own code trying to find the issue. A note should be made in the official documentation for FLfile.write().