Which programs? e-shop-published programs such as Pokemon, or user-created programs written in SmileBasic?
For e-shop programs, usually you go to the e-shop, find the update there and download it. For programs written in SmileBasic, get the new version's download key from the author, and use it to download the new version.
on this note I was thinking about that too so I was thinking of a standard to go by for the game i'm working on... on is to comeup with variable names that will not change when they save in the game for inventory, stat, heath,ect
that way when i update the game to a new version say
DT-ATOAMATLK_v1 and old ended with _v0 and they downloaded _1 it download as a new project so then they can copy the save file from _v0 too _v1 and after copy save file they can delete _v0 project and resume the game with project _1.