what about nand blocks corruption?
Not sure
Probably the SysNAND blocks corruptions.
I had some crashes or something with Retroarch already but nothing happened to my 3DS.
Was still able to boot it.
If something doesn't booted correctly (PastaCFW Coldboot / CTR Boot manager), I just removed the SD Card, booted my 3DS and made a normal shutdown.
After this, I reinserted the SD Card and everything worked again
EDIT:
Probably there's something while the boot-process which is clearing the RAM or whatever (reset stuff?) which is happen while booting SysNAND which isn't happening while booting EmuNAND:
Sometimes when PastaCFW / Coldboot + CTR_BootManager doesn't work correctly after leaving GBA VCs or shutdown 3DS while in SysNAND PastaCFW, I just have to boot SysNAND in Clean mode (without any Exploit-Stuff) and reboot the 3DS to get PastaCFW Coldboot + CTR_BootManager to work again.
But yea:
Never bricked my SysNAND while using RetroArch since the first 3DS-Nightly Build. And RetroArch crashed many times already.