The guide you are mentioning is for setting up arm9loaderhax, not just switching to Luma3DS. arm9loaderhax is not tied to one custom firmware, you could even have a setup to load Luma as a default custom firmware and load Gateway's custom firmware when a specific button is pressed if you wanted.
As
@cvskid said, you can already use Luma3DS with your EmuNAND to make sure that everything works (spoiler: it should work). Of course, you won't be able to use the Gateway mode from Luma3DS.
As for following the guide to set A9LH up, you can keep your EmuNAND and everything that goes with it. To keep it simple, here's what would happen:
Updating the EmuNAND to 11.0
-> Making a backup of it before formatting it
-> Downgrading it to 2.1 before it is copied to SysNAND
-> Getting necessary files and installing arm9loaderhax
-> Restoring your original backup to SysNAND
-> Deleting the EmuNAND (if you want).
Might sound scary, but the point is that at the end, you will be using your current EmuNAND as a main system.