I actually did change the altstage2. Before anything, I did everything intentionally, ShadowNAND was not the cause of the brick, I was, I wanted to brick my system. ShadowNAND just happen to be the tool I was using to brick it.
I wanted to test out a few different way to actually brick my system, so I made a back up and started working on it. Once it was bricked, I was actually intending to practice setting up a hard mod (I was going to buy the tools last week) and repair it myself. But ultimately scrapped the 2DS in favour of repairing my 3DS.
I would like to make it clear, that I wanted to kill my 2DS for the sake of personal science.
ShadowNAND was not the direct cause, but the indirect tool I used. It could have easily been SafeA9LHInstaller that I could have used. But considering the tool that was on my 2DS at the time was ShadowNAND installer, I used that instead.
Edit: On topic: arm9loaderhax.bin is working again