Recently, I've had problems with my NNID account and wish to make a new one on the same console. My question is, If I restart my NNID account, will my Omega Ruby download be safe, or will it also be deleted, even with the SD card removed?
You can make sure that your downloaded game is located on your SD card. When you reset your NNID account it shouldn't affect your SD card. To be safe you can remove your SD card before you reset your NNID