Do you mean basically just pulling out the current SD card, and sticking in the new blank one and doing no data movements of any kind? You'll just have 2 SD cards associated with that system. Not much will happen but sometimes it'll screw with some things like Streetpassing, Spotpassing, or other things that are logging games within the system. It's probably safer to just have everything on one SD card unless you have absolutely no intention of returning to what is on the first card. But either way it really doesn't matter and people do it all the time.
Sorry if I misunderstood...
Okay I did this and it's just fine, no PC needed:
>Select PC transfer.
>When the transfer process is done, turn off your system, just take your micro sd out of your old original 3DS system (Out of your standard SD card size adapter).
>Turn New 3DS off, take stylus out un-screw back.
>Insert SD card into your New 3DS.
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Topic: Is the SD card transfer necessary if you already have a micro SD?
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