The only thing I can think of that may have caused it to corrupt right at the finish line was a disconnect; whether it be the connection was lost on behalf of Windows or Mac, or the USB adapter became dislodged. Battery charge might play a role as well but I've never gotten to that point as my batteries always die in the heat of me playing with the damned thing.
Either way, to avoid having to go through every file again in the future you can save configuration files by going to the "Write Sounds" tab, and underneath the main window you'll see "You can also Save...", click save, name it whatever you'd like, and you'll never have to deal with that again.