Usually I avoid answering into topics that mention a year date in the title. The year has nothing to do with the question.
In this case I'll make an exeception since it is a topic of my main interest.
General problem is that homebrew and custom firmware allow to do things not intended by the manufacturer. The end user is not supposed to have full access and therefore is not able -- normally -- to damage the operating system (of course on any device things can go wrong).
Nintendo didn't think of a way of allowing the end user to reistall the stock software in case something goes wrong. To be fair spontanous damage is unlikely. I've interrupted firmware updates on purpose multiple times in a row on different progress. No success(?) in destroying anything.
With exploits we are able to break out of the cage and can therefore execute arbitrary code with highest privileges (ARM9 kernel). This is a bit like Unix/Linux user root or Windows Administrator (or even system). The usual advise of "not executing unknown software" and only use "trusted sources" sounds good, but generally is the opposite of what a homebrew user is going to do. The whole point of this is using
unauthorized software (like Nintendo calls anything not apporved by them).
A few ways of damaging the software on the internal memory (NAND):
- Using GodMode9 hexeditor to change raw data. Sadly I'm not making this up.
- Using GodMode9 to delete arbitrary files and folders on CTRNAND
- All in all playing around with GodMode9 and ignoring red warning screen
- Changing vital components (for example region changing) and uninstalling B9S afterwards
- Using FBI to delete titles marked in red (NAND titles)
- Forcing a NAND restore from a different console (=overwriting everything with garbage data)
- Playing around with the homebrew application "System Updater" to update or downgrade firmware
- Installing firmware for the wrong device (old type on new console or vice versa)
Again, these are just examples.
Generally 3DS homebrew/CFW is very advanced and safe. One has to do stupid things
on purpose to damage software, In most cases repair can be done by:
- Updating firmware with official updater (if safe mode still works)
- Restoring a known good NAND image (certain data has to be backed up before doing this). Don't do this unless really needed.
- This means having a good NAND image for the worst case is mandatory. Never skip the backup steps on 3ds.hacks.guide -- Store the image on multiple media
- CTRTransfer
- CTRTransfer Type D9 script
In case B9S is inaccessible (8046 blue screen, B9S uninstalled) an ntrboot cart is needed to boot into GodMode9.
In principle 3DS malware that can hardware(!) damage a console with no way to repair it is possible.