I have had some java moss randomly die off on me as well. I have noticed that when I move java moss from above the waterline to a submerged location, it often dies back(sometimes quite a bit) or simply "sits" for up to a few weeks before it starts growing again. I think it's like "crypt melt," something that often happens to the plant naturally and isn't really a big deal. People just think the plant is dying and toss it out(something of which I am guilty of!)...