I tried the original unhacked ROM with the hacked 1.2 update (didn't know how to unselect an update) and while I am fairly sure that would have caused problems in the game, it still managed to boot, which kinda rules out the CIA update as the culprit
Edit: Alright so now I tried properly removing the 1.2 CIA update. Same result: the original ROM boots, the hacked ROM does not. Your proposal gave me an idea, and I tried to decrypt the original ROM and then immediately repack it again without altering any files, and it turns out as a 2GB rom instead of the 4GB original. Since I didn't alter any files I am kinda stumped on where the other 2GB went. Obviously it will not boot, claiming a fatal error (so not the same issue as the hacked ROM that doesn't give any errors and is the correct 4GB size). I don't know if this is normal or maybe I have a corrupt version of the 3ds toolkit. Please advice :)
2nd Edit: I played around with my 1.2 CIA Update files. Turns out the original unhacked CIA supports a wrong region; Citra will remove the icon of the ROM (the original unhacked one in this case) and claim invalid region. Despite this it still boots (and I presume will also work during gameplay).
Ironically, the hacked CIA update based on the same file does not complain about any regional conflicts. It still boots, even with the unhacked ROM, but I don't know if this could cause some issues?
3rd Edit:
So to recap:
- My original ROM is the correct size of 4.294GB. It boots with or without the 1.2 Update.
- The hacked ROM is the exact same size but won't boot. Does not provide any errors, just gets stuck on a black screen when trying to boot with or without the 1.2 update
- My original 1.2 CIA update claims regional conflicts with the ROM, yet still boots and presumably also works during gameplay
- The hacked 1.2 CIA update does not claim regional conflicts despite being based on the same file as the original; still boots with the unhacked ROM. No difference on the hacked ROM
- Extracting and immediately rebuilding the original ROM without altering any files leaves it as a corrupt ROM of a peculiar 2 GB size. Gives a fatal error when trying to boot.
- Sidenote: I had to use the v10 hacking toolkit to make my update as the v9 didn't work. Seemingly no issues with the CIA hacking; everything points to the ROM hacking being the culprit