I've been working on a level for a couple months now. It was (I think) about a hundred screens. Today, it disappeared. I opened the editor, and there was nothing there besides the starting position. It was as if the whole level got deleted. All the custom tilesets I had were still there, however. I looked in the folder and found that the map.bin was still there, and was 10 KB big. I then tried replacing the map.bin with the map.bin from another level. Nothing happened. I also tried to run it from the game and got the same big void. I then opened the map.bin file in notepad. It was one big row of spaces. Typically when you open a map.bin, it's gibberish. It seems as though the map.bin got completely erased, leaving everything else intact. This happened before on one of my other levels. It was a test level though, so it didn't really matter, and I dismissed it as a glitch.
tl;dr. Backup your levels.