If you wan't to use a9lh there is no need to unlink Nands and even still all saves from digital games are in the SD card, and every save from a dsiware and VC will be copied to the sysnand backup. If you're gonna instal a9lh, there is no need unlink nands by formatting one or another. if you use sysupdater cia on emunand, only the emunand will be touched.
if else you want to use menuhax/browserhax. you can be on the go with linked nands, things are, if you by any case enter sysnand and not emunand, all the games that were installed from emunand will be deleted because sign cheks. Still, your saves from inside the nand are safe with 10.7 backup (hardmod) or 9.2 backup (menuhax/browserhax)
Then, if everyone go to read before i edited (as i fast readed the OP and then read the comments). There you go an unnecesary explanation on emunand setup and why sd card has to be formatted in order to set it up.
UNNECESARY EXPLANATION!!:
Setting up a Emunand without formatting isn't possible, as partitions that currently has a file system can't be resized.
If you need to setup a emunand to use menuhax, as said before, you HAVE to backup the Nintendo 3DS folder, or else you'll have to redownload/install everything again. because again, as said before by me, partitions that currently have a file system can't be resized as it will mess up all the data inside.
if else you need to setup a emunand to install arm9loaderhax, i kindly recommend you using a different sd card, mainly for comfort.
from my experience installing a9lh, you can do the whole thing with just 1 obligatory backup, which is your sysnand 9.2, even though, for security reasons hardmod your 3ds in order to get the 10.7 sysnand backup in case the downgrade to 9.2 goes wrong (even though it just happened to me 1 time so far).
Recapitulating: It's impossible to no format your sd card for setting up an emunand on it, it needs 2 partitions, the fat32 to save data, and the one used by emunand.
