update the emunand, not the sysnand.
if you update the sysnand, it's game over for you
If you're running menuhax+cfw, make sure your nands are unlinked.
If so, you can safely update your emunand without removing the sd
if you are a returing member to the scene and havn't touched your 3ds for a while, first thing you should do is update to 9.2. Follow this guide on how to update to 9.2.0. From there follow this guide to get the latest cfw.