Will do! But are you sure the two NANDs will be unlinked then?
You didn't say what you want to save, anyway I'll try to explain better.
I had some games installed into my sysnand, with saves too.
What I did:
1) Placed the microsd into my PC and made a backup copy of the Nintendo3DS folder.
2) Opened the gateway launcher (im not a GW user but you can launch the menu anyway) and selected the "format emunand" option.
NB: now you have an emunand that's linked to the sysnand.
3) Placed the microsd card into my PC and copied back the Nintendo3DS folder from my desktop into the microsd card
NB2: if you look at your Nintendo3DS folder, you'll see that inside you'll have the same "random numbered folder".
4) powered on the 3ds without the microsd card and did a sys format (dont know how it's named in english)
5) after the format and the power off, reinsert the microsd card into the 3ds and power on. It will does a new setup, creating folders.
Now your nands are unlinked, you can see opening the nintendo3ds folder and you will see two random numbered folders, the one with more GB weight is your emunand with games installed and the other is the sysnand.
Doing this way i had my games transferred from the sysnand into the emunand, with samegames too.