I know God Mode doesn't work with some attacks like, [Absorb x Panel to do x amount of damage], [Damage Panel], [Virus or Virus Panels], [Timer Panel]. You just have to play around those gimmicks.
I usually enable God mode and 1 hit kill/or autowin in the title screen menu.
I also make sure that I wasn't in a past battle before I closed the app (When you re-open the app and login, it says do you wish to resume your last battle) or when there is any new data pushes for micro updates.
If there is a data push, I'll restart the app afterwords and re enable what hack settings I want to use at the main menu.
And I always test to see if it's working first on 1-1 when I log in.
This is what I do each time.
Cheers.