This will completely remove CFW from your device, including Boot9Strap and Luma3DS, for the purpose of restoring the device to stock.
Any unsigned (illegitimate) games will be rendered unusable and can be manually removed using the Data Management section of the System Settings. Use a [save manager](https://github.com/J-D-K/JKSM/releases/latest) to backup any saves for these unsigned (illegitimate) games you care about.
This will not affect your NNID, any legitimately purchased games, or any saves for those legitimately purchased games.
Note that if you have any payload files other than `GodMode9.firm` in the `/luma/payloads/` folder on your SD card, holding (Start) on boot will display a "chainloader menu" where you will have to use the D-Pad and the (A) button to select "GodMode9" for these instructions.