So I figured out a simple trick to install clean CIA's to your sysnand on an SD that has an emunand partition.
What you need:
Hardware:
GW red card.
3DS exploitable by GW. (9.2 or lower)
Main Emunand SD Card. (that you already use for everything.)
A second SD card formatted to fat32.
GW microSD card.
Software:
--Some clean CIA's.
--Bigblue.3ds
--launcher.dat
Step 1.
remove your emunand card from your 3ds.
Step 2.
put it in your pc and put all those clean CIA's on there using your PC.
Step 3.
Place GW launcher.dat on the second SD card. (that's the only file you need on there.)
Step 4.
Place this launcher.dat SD card in your 3DS.
Step 5.
Place Bigblue.3ds on the GW sd card.
Run GW exploit as usual. (DO NOT INSTALL EMUNAND)
Step 6.
Boot gateway mode.
Step 7.
Remove SD Card.
Step 8.
Put your emunand SD Card back into the 3DS. (now with clean CIA's in the root)
Step 9.
Run big blue and install.
Step 10.
Now you have clean CIA's and Emunand CIA's all on one SD Card.
**Recommended that you have a hardmod when touching the sysnand.
What you need:
Hardware:
GW red card.
3DS exploitable by GW. (9.2 or lower)
Main Emunand SD Card. (that you already use for everything.)
A second SD card formatted to fat32.
GW microSD card.
Software:
--Some clean CIA's.
--Bigblue.3ds
--launcher.dat
Step 1.
remove your emunand card from your 3ds.
Step 2.
put it in your pc and put all those clean CIA's on there using your PC.
Step 3.
Place GW launcher.dat on the second SD card. (that's the only file you need on there.)
Step 4.
Place this launcher.dat SD card in your 3DS.
Step 5.
Place Bigblue.3ds on the GW sd card.
Run GW exploit as usual. (DO NOT INSTALL EMUNAND)
Step 6.
Boot gateway mode.
Step 7.
Remove SD Card.
Step 8.
Put your emunand SD Card back into the 3DS. (now with clean CIA's in the root)
Step 9.
Run big blue and install.
Step 10.
Now you have clean CIA's and Emunand CIA's all on one SD Card.
**Recommended that you have a hardmod when touching the sysnand.