This will completely remove CFW from your device, including Boot9Strap and Luma3DS, for the purpose of restoring the device to stock.
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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.
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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.