You just simply copy the entire content from your SD Card to any storage medium you wish to use. That's only efficient in case a repair center staff end up accidentally destroying your card for some reason.
If the repair center asked you to leave your SD Card in your 3DS, then better hope your system can turn on and access to System Transfer just fine. If that works, then you're pretty much guaranteed that if they should send you a new 3DS, it will have whatever you had in your original system.