I believe that once you’ve done the transfer, you can redownload the games that were on the New 3DS’s SD card from the eShop. However, I’ve never transferred to another 3DS that had anything preinstalled, so I couldn’t say for sure. Nintendo suggest that would be the case:

If I transfer from a console with a Nintendo Network ID registered to a console that has pre-intsalled software on the SD card, what happens to the pre-installed software?

Pre-installed software on the SD card can be re-downloaded from the Nintendo eShop after a system transfer is performed.

But then they did spell “installed” as “”intsalled”, and their SD transfer guide doesn’t completely work, so I don’t know if you should entirely trust them 🙂