The 3DS Guide tells you how. A quote from the guide:
So .. Follow the guide as if you were installing it on a stock 3DS with no CFW installed, and the steps later on will tell you how to transfer existing setup over, if wanted.
- If you have already hacked your 3DS before to get an EmuNAND setup, and would like to move the contents of your previous EmuNAND to your new SysNAND CFW, you should follow all instructions and restore your existing EmuNAND when prompted once you reach Installing arm9loaderhax.
I will try. Everybody keeps linking me to that site, I find it hard to read and navigate.
Luma CFW did fix my issue though.