Saves on the SD card are naturally console encrypted. Furthermore, you can’t load back an older version of the save; the internal memory of the 3DS keeps track of versions of the save, and prevents you from loading back an older version.
To avoid all of that, the simplest method (and also one we can explain to newbies easily) is for you to extract the save with CFW + homebrew.
and in case it hasn’t been mentioned enough, you can’t trade from 3DS to PC.