The multirom takes the save from the SD and plays with it.
When you save, it updates the save in the mSD at the moment.
When you shutdown or home+x, the save transfers back to the SD.
If you eject by accident, you should immediately put the red card mSD in a computer and see if the updated save is still there.
Launching the game after an eject will simply reload the SD save, deleting the updated save on the mSD.