No.
When you do a System Transfer, the target 3DS ends up EXACTLY like the original 3DS. Absolutely everything is transferred. DSiWare, 3DS and Virtual Console software, Ambassador status, system settings, Play Coins, Activity Log data… EVERYTHING.
Everything on the target 3DS system will be erased, so back up any photos or audio recordings saved to the internal memory to the SD card. Any saved games for DSiWare on the target system will be lost. The original 3DS will be erased, also. When you turn it on, it will be like it's being turned on for the first time.