I don't know how credible this info is, but from another forum:
QUOTE said:Well, Nintendo recently have added code to their latest SDK which lets flashcard developers add a check to their game to see if the game is running on a flashcard. Though it is up to the developer or not to use the code. Though since its in the SDK, the code itself is the same with every game and thanks to this, has made patching it relatively easy now. So its a matter of searching the games memory for the routine and patching it as the memory location of the routine is different every game.
Now what this code does is well, rather simple. It does a check for a memory region of the game below 8000h. On a normal DS game, if the game tries to access the memory below the 8000h range, it gets redirected to 8000h + offset. So for a real DS game, its impossible to access that memory which isn't true for a flashcard. So on a flashcard, if the check detects it can access that memory range, it returns true. Now its up to the developer on how to implement if the check returns true or false so how its handled differs for each game. Some games delete your saves while others prevent you from saving and some cause the game to show a screen after playing for a certain amount of time.