@Sono Could you destroy the charge controller with software?
The thing is, is that yes and no.
The MCU manages whether the PMIC should allow battery charge or not. The PMIC can't be destroyed by software (or at least, none that I know of, especially since only the MCU is connected to it), but the MCU can be "destroyed" via software. There isn't a functional MCU bricker out there though, so that's unlikely.
If the 3DS works, but it doesn't charge, and assuming the charger works, then there is only one thing that could be happening: battery lockout
Basically there is some code in MCU_FIRM which locks out certain batteries on certain consoles, and prevent charging it at all cost.
As for turning on the 3DS without a battery, I forgot what exactly you need to do, but you can hard-tie the middle pin to negative(?), and that should enable the 3DS to turn on, although it will NOT charge in that mode either, as it's a special mode intended for adapter-powered (not charger) 3DS units.