On rare occasions, "File -> Save Project" stops working and actually wipes out the entire squeaker-project file. There is no error message in the UI and the file contents will be completely erased. The project file still exists, but its completely empty and has no contents. I haven't found a way to reliably reproduce this, unfortunately.
EDIT: I was able to reproduce this with a small test project. I found that if I delete the zero-length corrupt project file and then save again, then it will be saved correctly. That still doesn't explain why it's getting corrupted in the first place, though.