I have an MK5 and only once I ran into this problem. I don't know what caused it but since it happened I have been backing up my saves more often. Zelda is the only game it happened to, odd.
It happened after I tried another game on the cart that was a different save type, then I went back to Zelda. I could have also used the soft-reset on Zelda to get back to the menu to try the other game too.
I can only suggest backing up your saves more often. Also do you have the latest firmware and set the save to 4Mbit?