Didn't see anyone respond to this. First, just wondering why you want to format.
If you follow Plailect's guide strictly, you can keep your games, saves, NNID, etc.
If you want to format but also want your saves, you could install from HBL you can use
https://gbatemp.net/threads/svdt-save-data-explorer-manager.396562/ or,
https://gbatemp.net/threads/release-jks-savemanager-homebrew-cia-save-manager.413143/ once you have FBI installed and run it in emuNAND before you do any formatting.
Then, if you want to have a clean format, in part IV (Restoring the System) of section 4 (Getting the OTP), choose emuNAND_formatted.bin instead of emuNAND_original.bin. (I have done this part before on a system that had no games or saves because I wanted the FBI icon to look right instead of looking like the H&S "!" icon and for some reason this only showed up that way after running TinyFormat)
Once you complete the guide you can reinstall your games, start them once to initialize save data, and then restore your saves to them.