Updating is usually safe when you have custom firmware, but Nintendo makes sure to keep the CFW developers on their feet by applying patches that break the boot sequence. Here is how to safely update.
Note: This guide is for the following devices
OLD 3DS
OLD 3DS XL
OLD 2DS
NEW 3DS
NEW 3DS XL
NEW 2DS XL
To begin make sure you are connected to the internet or the tools we are going to use wont work if that all sorted then we can begin with the update.
Start by opening the Luma CFW Updater and selecting update to the latest stable release once you have pressed A you will need to hold X and press A at the same time to allow it to update the SD card less CFW.
C > Users > youruserlocation > Appdata > Roaming > Microsoft > Windows > Themes
Once you have updated Luma CFW the console should reboot and a menu should open up scroll down to "show NAND or user string in System Settings" and press A then START.
Finally go to system settings once the 3DS boots and perform a system update by going into System Settings > Other Settings > Page 4 > System Update
agree to the terms and conditions and update like you normally would when the update finishes the console should reboot and you will then be on the latest version.
Thanks for reading.