Well it just happened again.
This time I noticed it happen in a sense. When I clicked save I got a pop-up that said unable to save
Then it proceeded to save. It showed the progress bar and looked to have completed correctly. But when I look at the file in my file browser it says it is only 22bytes again. If I click save again I get the same pop-up and 22byte file. Fritzing thinks it has saved the file and no longer shows the * next to the file name in the window title. The board, schematic etc also all still work as long as the program stays open but you can't actually save it.
I checked in my hidden Fritzing config directory and indeed the fzz folder was empty but there was a temp folder in the backup directory. I made a copy of this folder just in case.
In case I needed to remember any changes I made since backing up yesterday I copied the PCB view to a new window and saved it as well as doing the same to the schematic.
I then decided to close Fritzing and it didn't ask me to save or complain in any way. I proceeded to check the backup folder and Fritzing had deleted the backup it had created (I assume because it thought it had saved successfully). I copied the backup of the backup that I had made back into the folder, opened Fritzing and it asked me if I wanted to recover my file. I selected recover and wrote over the 22 byte file.
In the end I had lost nothing.
Edit: Removed comment about posting in the wrong thread.