Yes. Very much possible. If you follow the guide.. everything currently installed on Emunand will be present on your Sysnand.
I was worried about this too. But even my save games are intact - without even a backup of those. I was surprised.
That's odd. I know you back-up your emunand, but I always thought emunand was just the partition where the system was stored, not where the game are located.
It may be because the emunand loads the Nintendo 3DS folder that had the games in it, but I'm probably wrong.
