Just not, you will now be loosing nds/dsi game support as you will no longer have a valid twl header (unless luma has some new patch to save the arses of all these people who decide that nand backups aren't important for them)
@d0k3 I would like to suggest you dump all the essential files to a totally out of the way location that people are unlikely to just delete all willynilly somewhere like "Nintendo 3ds/DO NOT DELETE ME".......although I'm sure people will still find a way to screw thing up
, oh and maybe for the nand dump made during ctrtransfer to have a button combo to skip it, so people have to be consciously forcing the nand backup to not happen rather than just accidentally hitting B, and last thing would be making the ctrtransfer nand backup have a console unique name like the rest of the backup files do, I think that would cover most genuine accidental screw up, any beyond that and it's a guaranteed end user issue