What should I know if I transfer my data from a normal 3ds to a modded one?

What i wanna do is transfer my data from my vanilla 3ds to a molded one so I can back up my saves on my digital games. I know modding a 3ds comes with programs, but would those programs still be there if I transfered everything? Also, if i return them to an unmoved 3ds, who those homebrew program still be there?

If you got other things to mention, please do.