You will not be able to perform a system transfer if there is any Nintendo Network ID already linked to the target system.
After transferring data, all data on the source system will be deleted.
Note: With the exception of Nintendo DSiWare, the data in the target system's system memory (e.g. pre-installed application save data) will be deleted and overwritten with the data from the source system. If you have data such as photos and recordings in the target system saved and wish to keep them after the transfer, copy these to a microSD card first.
Download software precautions:
Data stored on the target system's microSD card, such as Nintendo 3DS download software and its save data, will not be usable after the transfer. The software can be re-downloaded from Nintendo eShop.
Nintendo DSiWare and its save data on the target system's microSD card should be moved to the target system's system memory before the transfer. It will then remain usable after the transfer.
If the same download software has been downloaded on both systems, its data on the target system's account activity will be deleted and replaced with the data from the source system. Also, the old save data on the target system with no longer be usable.
Nintendo eShop funds precautions:
If the total Nintendo eShop funds of the source and target systems exceed the maximum allowed, the system transfer will not proceed.