First statement and already feel disaster
and I was right. If this is V2, then you have completely fucked up.
Now you don't have any other option as you have fucked up boot0/boot1.
Don't use Choi if you can. Don't use Choi on V2/Lite at all as it's not designed to work with them and it will always fuck up your boot0/boot1
Issue normally is omitted by using SX OS which implemented hacks to boot0/boot1 to avoid issue with those, but on Atmosphere it won't work at all. So you have also triggered corruption while updating and because Choi doesn't check if installed update is not corrupted, then you got this.