choidujournx is outdated. As Hayato213 said above use Daybreak instead. You should find daybreak is already installed as part of Atmosphere and is available in the homebrew menu. It's very easy to use and you just need the same update files you would have used with choidujournx, again as Hayato213 mentioned.
You'll probably want to update your sigpatches after the firmware update too.
I did the same process recently and upgraded from 10.0.? (can't remember exactly) to 12.0.3 using daybreak for the first time. It was simple.
How do I update the sigpatches? I see there is an app available aio switch updater. It can update it, but my switch has the internet blocked so that one wont work for me. I will need to do it manually.