To confirm, I had my save disappear with flash 4mbit as well, and am now trying flash 2mbit. I lost it around the 6th or 7th mission after some rather heavy repeating of the second training level.
I'm not convinced the n-card handles the flash 4mbit savetype 100% after once losing a zelda save in similar circumstances (lots of powering off and on in quick succession).
(this is with the latest n-card firmware with dldi update from dsgba.com)