This happened to me last night at a show a few hours before I was supposed to play! Luckily (and because I am anal about having back-ups of everything), I had brought my netbook with me which had backups. So I quickly dumped the .sav files back on the cart and was ok. However I'd like to try and pin down what caused this.
What happened: Now this only happened to the song file I had open. The chains all looked correct but upon entering them, the phrases were completely wrong. Wrong phrases, wrong placements, etc. Nothing that could've been accidental on my part. No notes inside phrases too.
What I had been doing: Two gba sp's. Two ems carts. They were already on when I plugged the link cable in.
Currently, my only guess is that having the gba's on, with the carts in and then plugging the link cable in is what caused this.
This wasn't a huge deal but still unnerving. Definitely bringing my netbook to every show.