iconv to the rescue
Unfortunately, I must have accidentally saved the file before I was able to exit the Ommwriter, because when I tried to reopen the file in TextEdit I got the same result. I was pretty sure I was encountering an encoding problem. Time for iconv. The default encoding on my Mac is UTF-8 so I tried something like:
iconv -f UTF-8 -t UTF-16 foo.txt
And lo and behold I got my text back. After investigating the problem for a little bit I found out that the problem occurs when the text contains characters outside the [A-Z] and [a-z] range, for example an ö.
Anyways, after this initial hiccup, I have to admit I am positively surprised about Ommwriter. The fact that all distractions are removed from the screen really helps focusing on the actual task of writing. I also like that there is no spell checker. You are actually focusing on writing and not proof reading. Most surprised I was, however, by the fact that audible keyboard strokes actually really help the writing process.