Yes, it should still be there. Mine has stayed without any problems after putting it into the computer a few times to add games and change M3 skins.
From my understanding (and I could be wrong), with a normal, retail-bought game, the friend code is stored in the game card. I believe this is what the game tells you when you register it for the first time in WFC. But with flash devices, the saved information that would normally be in the game card gets saved to the flash device.
If you're worried about loosing your friend code because you delete your save or use a different save, the friend code is generated based on the game/rom and the DS. As long as those don't change, it should stay the same. Even if a save already has another friend code, it gets overwritten with your code.
As I said, I could be wrong. I've only had my M3 since Saturday and it's my first NDS flashing device, but I've spent quite a bit of time reading up on it while I was waiting for it to arrive. Also the circumstances may be different for other devices (G6, EZ-Flash, Supercard, etc), as I have little knowledge of how they work, but I would image that it's similar.